18 Apr
2017
18 Apr
'17
9:21 p.m.
Hello freesurfer, I am trying to run mri_glmfit with the --table flag. My aparc_lh_thick_stats.txt contain entorhinal and parahippocampal thickness values for 32 subjects. I ran the glm command and received an error. Please, how can i solve this issue? I have included my command, fsgd file, contrast matrix and error below. Thanks Best, Paul
GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir
ERROR= "gdfRead(): reading age.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 39.9375 17.3312
Class Means of each Continuous Variable
1 Group1 35.6316
2 Group2 46.2308
INFO: gd2mtx_method is dods
Reading source surface /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.984375
AvgVtxArea 0.399269
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Users/MiracleOz/Documents/improvervsdeclinermri
cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir
sysname Darwin
hostname MacBook-Pro.local
machine x86_64
user MiracleOz
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
logyflag 0
usedti 0
FSGD age.fsgd
labelmask /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.thickness.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.thickness.glmdir
Loading y from /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
Found 66 data colums
Found 0 data rows
INFO: gd2mtx_method is dods
Saving design matrix to lh.thickness.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 32.2165
Matrix condition is 20734.7
Found 149955 points in label.
ERROR: mri_reshape: number of elements cannot change
nv1 = 163842, nv1 = 66
search space = 82219.962936
ERROR: dimension mismatch between y and X.
y has 0 inputs, X has 32 rows."
FSGD file: GroupDescriptorFile 1
Title MOT
Class Group1
Class Group2
Variables Age
Input 01053p Group1 23
Input 01054p Group1 43
Input 01061p Group2 39
Input 01062p Group2 19
Input 01074p Group2 28
.............. (I have more participants)
CONTRAST MATRIX: 1 -1 0 0
18 Apr
18 Apr
9:51 p.m.
Don't include --surf fsaverage lh. It thinks the input is a surface, not a table
On 4/18/17 9:21 PM, miracle ozzoude wrote:
Hello freesurfer, I am trying to run mri_glmfit with the --table flag. My aparc_lh_thick_stats.txt contain entorhinal and parahippocampal thickness values for 32 subjects. I ran the glm command and received an error. Please, how can i solve this issue? I have included my command, fsgd file, contrast matrix and error below. Thanks Best, Paul
GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir
ERROR= "gdfRead(): reading age.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 39.9375 17.3312
Class Means of each Continuous Variable
1 Group1 35.6316
2 Group2 46.2308
INFO: gd2mtx_method is dods
Reading source surface /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.984375
AvgVtxArea 0.399269
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Users/MiracleOz/Documents/improvervsdeclinermri
cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir
sysname Darwin
hostname MacBook-Pro.local
machine x86_64
user MiracleOz
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
logyflag 0
usedti 0
FSGD age.fsgd
labelmask /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.thickness.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.thickness.glmdir
Loading y from /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
Found 66 data colums
Found 0 data rows
INFO: gd2mtx_method is dods
Saving design matrix to lh.thickness.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 32.2165
Matrix condition is 20734.7
Found 149955 points in label.
ERROR: mri_reshape: number of elements cannot change
nv1 = 163842, nv1 = 66
search space = 82219.962936
ERROR: dimension mismatch between y and X.
y has 0 inputs, X has 32 rows."
FSGD file: GroupDescriptorFile 1
Title MOT
Class Group1
Class Group2
Variables Age
Input 01053p Group1 23
Input 01054p Group1 43
Input 01061p Group2 39
Input 01062p Group2 19
Input 01074p Group2 28
.............. (I have more participants)
CONTRAST MATRIX: 1 -1 0 0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
10:03 p.m.
You have a table of data, so no template is needed. If you put the --surf before the --table, it probably runs, but it will ignore the surface
On 4/18/17 9:58 PM, miracooloz@gmail.com wrote:
Thanks doug. Does it mean when using the --table flag, you can't use the fsaverage template? I came across several post in the forum that used "--surf fsaverage lh " and it worked. Best, Paul
Sent from my BlackBerry 10 smartphone. *From: *Douglas Greve *Sent: *Tuesday, April 18, 2017 9:52 PM *To: *freesurfer@nmr.mgh.harvard.edu *Reply To: *Freesurfer support list *Subject: *Re: [Freesurfer] mri_glmfit error with aparc table flag
Don't include --surf fsaverage lh. It thinks the input is a surface, not a table
On 4/18/17 9:21 PM, miracle ozzoude wrote:
Hello freesurfer, I am trying to run mri_glmfit with the --table flag. My aparc_lh_thick_stats.txt contain entorhinal and parahippocampal thickness values for 32 subjects. I ran the glm command and received an error. Please, how can i solve this issue? I have included my command, fsgd file, contrast matrix and error below. Thanks Best, Paul
GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir
ERROR= "gdfRead(): reading age.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 39.9375 17.3312
Class Means of each Continuous Variable
1 Group1 35.6316
2 Group2 46.2308
INFO: gd2mtx_method is dods
Reading source surface /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.984375
AvgVtxArea 0.399269
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Users/MiracleOz/Documents/improvervsdeclinermri
cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir
sysname Darwin
hostname MacBook-Pro.local
machine x86_64
user MiracleOz
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
logyflag 0
usedti 0
FSGD age.fsgd
labelmask /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.thickness.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.thickness.glmdir
Loading y from /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
Found 66 data colums
Found 0 data rows
INFO: gd2mtx_method is dods
Saving design matrix to lh.thickness.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 32.2165
Matrix condition is 20734.7
Found 149955 points in label.
ERROR: mri_reshape: number of elements cannot change
nv1 = 163842, nv1 = 66
search space = 82219.962936
ERROR: dimension mismatch between y and X.
y has 0 inputs, X has 32 rows."
FSGD file: GroupDescriptorFile 1
Title MOT
Class Group1
Class Group2
Variables Age
Input 01053p Group1 23
Input 01054p Group1 43
Input 01061p Group2 39
Input 01062p Group2 19
Input 01074p Group2 28
.............. (I have more participants)
CONTRAST MATRIX: 1 -1 0 0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
11:31 p.m.
Hello Doug, I tried it without "--surf fsaverage lh" but i still get error. Thanks Paul
cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --cortex --glmdir lh.thickness.glmdir
sysname Darwin
hostname MacBook-Pro.local
machine x86_64
user MiracoolOz
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
logyflag 0
usedti 0
FSGD age.fsgd
glmdir lh.thickness.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.thickness.glmdir
Loading y from /Users/MiracoolOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
Found 66 data colums
Found 0 data rows
INFO: gd2mtx_method is dods
Saving design matrix to lh.thickness.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 32.2165
Matrix condition is 20734.7
search space = 66.000000
ERROR: dimension mismatch between y and X.
y has 0 inputs, X has 32 rows.
On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
You have a table of data, so no template is needed. If you put the --surf before the --table, it probably runs, but it will ignore the surface
On 4/18/17 9:58 PM, miracooloz@gmail.com wrote:
Thanks doug. Does it mean when using the --table flag, you can't use the fsaverage template? I came across several post in the forum that used "--surf fsaverage lh " and it worked. Best, Paul
Sent from my BlackBerry 10 smartphone. *From: *Douglas Greve *Sent: *Tuesday, April 18, 2017 9:52 PM *To: *freesurfer@nmr.mgh.harvard.edu *Reply To: *Freesurfer support list *Subject: *Re: [Freesurfer] mri_glmfit error with aparc table flag
Don't include --surf fsaverage lh. It thinks the input is a surface, not a table
On 4/18/17 9:21 PM, miracle ozzoude wrote:
Hello freesurfer, I am trying to run mri_glmfit with the --table flag. My aparc_lh_thick_stats.txt contain entorhinal and parahippocampal thickness values for 32 subjects. I ran the glm command and received an error. Please, how can i solve this issue? I have included my command, fsgd file, contrast matrix and error below. Thanks Best, Paul
GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir
ERROR= "gdfRead(): reading age.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 39.9375 17.3312
Class Means of each Continuous Variable
1 Group1 35.6316
2 Group2 46.2308
INFO: gd2mtx_method is dods
Reading source surface /Users/MiracleOz/Documents/improvervsdeclinermri/ fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.984375
AvgVtxArea 0.399269
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Users/MiracleOz/Documents/improvervsdeclinermri
cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir
sysname Darwin
hostname MacBook-Pro.local
machine x86_64
user MiracleOz
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_ lh_thick_stats.txt
logyflag 0
usedti 0
FSGD age.fsgd
labelmask /Users/MiracleOz/Documents/improvervsdeclinermri/ fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.thickness.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.thickness.glmdir
Loading y from /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_ lh_thick_stats.txt
Found 66 data colums
Found 0 data rows
INFO: gd2mtx_method is dods
Saving design matrix to lh.thickness.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 32.2165
Matrix condition is 20734.7
Found 149955 points in label.
ERROR: mri_reshape: number of elements cannot change
nv1 = 163842, nv1 = 66
search space = 82219.962936
ERROR: dimension mismatch between y and X.
y has 0 inputs, X has 32 rows."
FSGD file: GroupDescriptorFile 1
Title MOT
Class Group1
Class Group2
Variables Age
Input 01053p Group1 23
Input 01054p Group1 43
Input 01061p Group2 39
Input 01062p Group2 19
Input 01074p Group2 28
.............. (I have more participants)
CONTRAST MATRIX: 1 -1 0 0
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
19 Apr
19 Apr
10:05 a.m.
Hello Doug, It worked. The issue was due to formatting error with the aparc file. Also, I was trying to visualize the result on the surface using freeview -f fsaverage/lh.pial -viewport 3d (clicking overlay on freeview and loading the sig.mgh). However, i got an error " failed to display overlay". How can I visualize the result? Thanks Best, Paul
On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
You have a table of data, so no template is needed. If you put the --surf before the --table, it probably runs, but it will ignore the surface
On 4/18/17 9:58 PM, miracooloz@gmail.com wrote:
Thanks doug. Does it mean when using the --table flag, you can't use the fsaverage template? I came across several post in the forum that used "--surf fsaverage lh " and it worked. Best, Paul
Sent from my BlackBerry 10 smartphone. *From: *Douglas Greve *Sent: *Tuesday, April 18, 2017 9:52 PM *To: *freesurfer@nmr.mgh.harvard.edu *Reply To: *Freesurfer support list *Subject: *Re: [Freesurfer] mri_glmfit error with aparc table flag
Don't include --surf fsaverage lh. It thinks the input is a surface, not a table
On 4/18/17 9:21 PM, miracle ozzoude wrote:
Hello freesurfer, I am trying to run mri_glmfit with the --table flag. My aparc_lh_thick_stats.txt contain entorhinal and parahippocampal thickness values for 32 subjects. I ran the glm command and received an error. Please, how can i solve this issue? I have included my command, fsgd file, contrast matrix and error below. Thanks Best, Paul
GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir
ERROR= "gdfRead(): reading age.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 39.9375 17.3312
Class Means of each Continuous Variable
1 Group1 35.6316
2 Group2 46.2308
INFO: gd2mtx_method is dods
Reading source surface /Users/MiracleOz/Documents/improvervsdeclinermri/ fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.984375
AvgVtxArea 0.399269
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Users/MiracleOz/Documents/improvervsdeclinermri
cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir
sysname Darwin
hostname MacBook-Pro.local
machine x86_64
user MiracleOz
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_ lh_thick_stats.txt
logyflag 0
usedti 0
FSGD age.fsgd
labelmask /Users/MiracleOz/Documents/improvervsdeclinermri/ fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.thickness.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.thickness.glmdir
Loading y from /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_ lh_thick_stats.txt
Found 66 data colums
Found 0 data rows
INFO: gd2mtx_method is dods
Saving design matrix to lh.thickness.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 32.2165
Matrix condition is 20734.7
Found 149955 points in label.
ERROR: mri_reshape: number of elements cannot change
nv1 = 163842, nv1 = 66
search space = 82219.962936
ERROR: dimension mismatch between y and X.
y has 0 inputs, X has 32 rows."
FSGD file: GroupDescriptorFile 1
Title MOT
Class Group1
Class Group2
Variables Age
Input 01053p Group1 23
Input 01054p Group1 43
Input 01061p Group2 39
Input 01062p Group2 19
Input 01074p Group2 28
.............. (I have more participants)
CONTRAST MATRIX: 1 -1 0 0
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
1:33 p.m.
It is a table of data, so you can't visualize it directly on anything. You can try using annotval2surfoverlay.m to create a surface overlay of the data.
On 04/19/2017 10:05 AM, miracle ozzoude wrote:
Hello Doug, It worked. The issue was due to formatting error with the aparc file. Also, I was trying to visualize the result on the surface using freeview -f fsaverage/lh.pial -viewport 3d (clicking overlay on freeview and loading the sig.mgh). However, i got an error " failed to display overlay". How can I visualize the result? Thanks Best, Paul
On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You have a table of data, so no template is needed. If you put the --surf before the --table, it probably runs, but it will ignore the surface On 4/18/17 9:58 PM, miracooloz@gmail.com <mailto:miracooloz@gmail.com> wrote:Thanks doug. Does it mean when using the --table flag, you can't use the fsaverage template? I came across several post in the forum that used "--surf fsaverage lh " and it worked. Best, Paul Sent from my BlackBerry 10 smartphone. *From: *Douglas Greve *Sent: *Tuesday, April 18, 2017 9:52 PM *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Reply To: *Freesurfer support list *Subject: *Re: [Freesurfer] mri_glmfit error with aparc table flag Don't include --surf fsaverage lh. It thinks the input is a surface, not a table On 4/18/17 9:21 PM, miracle ozzoude wrote:Hello freesurfer, I am trying to run mri_glmfit with the --table flag. My aparc_lh_thick_stats.txt contain entorhinal and parahippocampal thickness values for 32 subjects. I ran the glm command and received an error. Please, how can i solve this issue? I have included my command, fsgd file, contrast matrix and error below. Thanks Best, Paul GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir ERROR= "gdfRead(): reading age.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 39.9375 17.3312 Class Means of each Continuous Variable 1 Group1 35.6316 2 Group2 46.2308 INFO: gd2mtx_method is dods Reading source surface /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Users/MiracleOz/Documents/improvervsdeclinermri cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir sysname Darwin hostname MacBook-Pro.local machine x86_64 user MiracleOz FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt logyflag 0 usedti 0 FSGD age.fsgd labelmask /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.thickness.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.thickness.glmdir Loading y from /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt Found 66 data colums Found 0 data rows INFO: gd2mtx_method is dods Saving design matrix to lh.thickness.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 32.2165 Matrix condition is 20734.7 Found 149955 points in label. ERROR: mri_reshape: number of elements cannot change nv1 = 163842, nv1 = 66 search space = 82219.962936 ERROR: dimension mismatch between y and X. y has 0 inputs, X has 32 rows." FSGD file: GroupDescriptorFile 1 Title MOT Class Group1 Class Group2 Variables Age Input 01053p Group1 23 Input 01054p Group1 43 Input 01061p Group2 39 Input 01062p Group2 19 Input 01074p Group2 28 .............. (I have more participants) CONTRAST MATRIX: 1 -1 0 0 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
1:42 p.m.
Thanks Doug. However, I am running freesurfer analysis on my personal computer and I don't have matlab. Also, I don't know how this matlab script works/ matlab works. Any instructions on how to use it or alternate? Please and thank you. Best, Paul.
On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
It is a table of data, so you can't visualize it directly on anything. You can try using annotval2surfoverlay.m to create a surface overlay of the data.
On 04/19/2017 10:05 AM, miracle ozzoude wrote:
Hello Doug, It worked. The issue was due to formatting error with the aparc file. Also, I was trying to visualize the result on the surface using freeview -f fsaverage/lh.pial -viewport 3d (clicking overlay on freeview and loading the sig.mgh). However, i got an error " failed to display overlay". How can I visualize the result? Thanks Best, Paul
On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You have a table of data, so no template is needed. If you put the --surf before the --table, it probably runs, but it will ignore the surface On 4/18/17 9:58 PM, miracooloz@gmail.com <mailto:miracooloz@gmail.com> wrote:Thanks doug. Does it mean when using the --table flag, you can't use the fsaverage template? I came across several post in the forum that used "--surf fsaverage lh " and it worked. Best, Paul Sent from my BlackBerry 10 smartphone. *From: *Douglas Greve *Sent: *Tuesday, April 18, 2017 9:52 PM *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Reply To: *Freesurfer support list *Subject: *Re: [Freesurfer] mri_glmfit error with aparc table flag Don't include --surf fsaverage lh. It thinks the input is a surface, not a table On 4/18/17 9:21 PM, miracle ozzoude wrote:Hello freesurfer, I am trying to run mri_glmfit with the --table flag. My aparc_lh_thick_stats.txt contain entorhinal and parahippocampal thickness values for 32 subjects. I ran the glm command and received an error. Please, how can i solve this issue? I have included my command, fsgd file, contrast matrix and error below. Thanks Best, Paul GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir ERROR= "gdfRead(): reading age.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 39.9375 17.3312 Class Means of each Continuous Variable 1 Group1 35.6316 2 Group2 46.2308 INFO: gd2mtx_method is dods Reading source surface /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white
Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Users/MiracleOz/Documents/improvervsdeclinermri cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir sysname Darwin hostname MacBook-Pro.local machine x86_64 user MiracleOz FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
logyflag 0 usedti 0 FSGD age.fsgd labelmask /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label
maskinv 0 glmdir lh.thickness.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.thickness.glmdir Loading y from /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
Found 66 data colums Found 0 data rows INFO: gd2mtx_method is dods Saving design matrix to lh.thickness.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 32.2165 Matrix condition is 20734.7 Found 149955 points in label. ERROR: mri_reshape: number of elements cannot change nv1 = 163842, nv1 = 66 search space = 82219.962936 ERROR: dimension mismatch between y and X. y has 0 inputs, X has 32 rows." FSGD file: GroupDescriptorFile 1 Title MOT Class Group1 Class Group2 Variables Age Input 01053p Group1 23 Input 01054p Group1 43 Input 01061p Group2 39 Input 01062p Group2 19 Input 01074p Group2 28 .............. (I have more participants) CONTRAST MATRIX: 1 -1 0 0 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
1:47 p.m.
Sorry, I don't have another solution for you.
On 04/19/2017 01:42 PM, miracle ozzoude wrote:
Thanks Doug. However, I am running freesurfer analysis on my personal computer and I don't have matlab. Also, I don't know how this matlab script works/ matlab works. Any instructions on how to use it or alternate? Please and thank you. Best, Paul.
On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is a table of data, so you can't visualize it directly on anything. You can try using annotval2surfoverlay.m to create a surface overlay of the data. On 04/19/2017 10:05 AM, miracle ozzoude wrote: > Hello Doug, > It worked. The issue was due to formatting error with the aparc file. > Also, I was trying to visualize the result on the surface using > freeview -f fsaverage/lh.pial -viewport 3d (clicking overlay on > freeview and loading the sig.mgh). However, i got an error " failed to > display overlay". How can I visualize the result? Thanks > Best, > Paul > > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > You have a table of data, so no template is needed. If you put the > --surf before the --table, it probably runs, but it will ignore > the surface > > > On 4/18/17 9:58 PM, miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> wrote: >> Thanks doug. Does it mean when using the --table flag, you can't >> use the fsaverage template? I came across several post in the >> forum that used "--surf fsaverage lh " and it worked. >> Best, >> Paul >> >> Sent from my BlackBerry 10 smartphone. >> *From: *Douglas Greve >> *Sent: *Tuesday, April 18, 2017 9:52 PM >> *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >> *Reply To: *Freesurfer support list >> *Subject: *Re: [Freesurfer] mri_glmfit error with aparc table flag >> >> >> Don't include --surf fsaverage lh. It thinks the input is a >> surface, not a table >> >> >> >> On 4/18/17 9:21 PM, miracle ozzoude wrote: >>> Hello freesurfer, >>> I am trying to run mri_glmfit with the --table flag. My >>> aparc_lh_thick_stats.txt contain entorhinal and parahippocampal >>> thickness values for 32 subjects. I ran the glm command and >>> received an error. Please, how can i solve this issue? I have >>> included my command, fsgd file, contrast matrix and error below. >>> Thanks >>> Best, >>> Paul >>> >>> GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex >>> --glmdir lh.thickness.glmdir >>> >>> >>> ERROR= "gdfRead(): reading age.fsgd >>> >>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >>> >>> Continuous Variable Means (all subjects) >>> >>> 0 Age 39.9375 17.3312 >>> >>> Class Means of each Continuous Variable >>> >>> 1 Group1 35.6316 >>> >>> 2 Group2 46.2308 >>> >>> INFO: gd2mtx_method is dods >>> >>> Reading source surface >>> /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white >>> >>> Number of vertices 163842 >>> >>> Number of faces 327680 >>> >>> Total area 65416.984375 >>> >>> AvgVtxArea 0.399269 >>> >>> AvgVtxDist 0.721953 >>> >>> StdVtxDist 0.195470 >>> >>> >>> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ >>> >>> cwd /Users/MiracleOz/Documents/improvervsdeclinermri >>> >>> cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex >>> --glmdir lh.thickness.glmdir >>> >>> sysname Darwin >>> >>> hostname MacBook-Pro.local >>> >>> machine x86_64 >>> >>> user MiracleOz >>> >>> FixVertexAreaFlag = 1 >>> >>> UseMaskWithSmoothing 1 >>> >>> OneSampleGroupMean 0 >>> >>> y >>> /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt >>> >>> logyflag 0 >>> >>> usedti 0 >>> >>> FSGD age.fsgd >>> >>> labelmask >>> /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label >>> >>> maskinv 0 >>> >>> glmdir lh.thickness.glmdir >>> >>> IllCondOK 0 >>> >>> ReScaleX 1 >>> >>> DoFFx 0 >>> >>> Creating output directory lh.thickness.glmdir >>> >>> Loading y from >>> /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt >>> >>> Found 66 data colums >>> >>> Found 0 data rows >>> >>> INFO: gd2mtx_method is dods >>> >>> Saving design matrix to lh.thickness.glmdir/Xg.dat >>> >>> Computing normalized matrix >>> >>> Normalized matrix condition is 32.2165 >>> >>> Matrix condition is 20734.7 >>> >>> Found 149955 points in label. >>> >>> ERROR: mri_reshape: number of elements cannot change >>> >>> nv1 = 163842, nv1 = 66 >>> >>> search space = 82219.962936 >>> >>> ERROR: dimension mismatch between y and X. >>> >>> y has 0 inputs, X has 32 rows." >>> >>> FSGD file: GroupDescriptorFile 1 >>> >>> Title MOT >>> >>> Class Group1 >>> >>> Class Group2 >>> >>> Variables Age >>> >>> Input 01053p Group1 23 >>> >>> Input 01054p Group1 43 >>> >>> Input 01061p Group2 39 >>> >>> Input 01062p Group2 19 >>> >>> Input 01074p Group2 28 >>> >>> .............. (I have more participants) >>> >>> >>> CONTRAST MATRIX: 1 -1 0 0 >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > _______________________________________________ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> The > information in this e-mail is intended only for the person to whom > it is addressed. If you believe this e-mail was sent to you in > error and the e-mail contains patient information, please contact > the Partners Compliance HelpLine at > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> . If the e-mail was sent > to you in error but does not contain patient information, please > contact the sender and properly dispose of the e-mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
3:33 p.m.
Hello Doug, Do you think writing the script with octave can substitute for matlab? I am using FS v6.0 and I have the annotval2surfoverlay.m. Thanks Best, Paul
On Wed, Apr 19, 2017 at 1:47 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Sorry, I don't have another solution for you.
On 04/19/2017 01:42 PM, miracle ozzoude wrote:
Thanks Doug. However, I am running freesurfer analysis on my personal computer and I don't have matlab. Also, I don't know how this matlab script works/ matlab works. Any instructions on how to use it or alternate? Please and thank you. Best, Paul.
On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is a table of data, so you can't visualize it directly onanything.
You can try using annotval2surfoverlay.m to create a surface overlay of the data. On 04/19/2017 10:05 AM, miracle ozzoude wrote: > Hello Doug, > It worked. The issue was due to formatting error with the aparc file. > Also, I was trying to visualize the result on the surface using > freeview -f fsaverage/lh.pial -viewport 3d (clicking overlay on > freeview and loading the sig.mgh). However, i got an error " failed to > display overlay". How can I visualize the result? Thanks > Best, > Paul > > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > You have a table of data, so no template is needed. If you put the > --surf before the --table, it probably runs, but it will ignore > the surface > > > On 4/18/17 9:58 PM, miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>wrote:
>> Thanks doug. Does it mean when using the --table flag, you can't >> use the fsaverage template? I came across several post in the >> forum that used "--surf fsaverage lh " and it worked. >> Best, >> Paul >> >> Sent from my BlackBerry 10 smartphone. >> *From: *Douglas Greve >> *Sent: *Tuesday, April 18, 2017 9:52 PM >> *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >> *Reply To: *Freesurfer support list >> *Subject: *Re: [Freesurfer] mri_glmfit error with aparc table flag >> >> >> Don't include --surf fsaverage lh. It thinks the input is a >> surface, not a table >> >> >> >> On 4/18/17 9:21 PM, miracle ozzoude wrote: >>> Hello freesurfer, >>> I am trying to run mri_glmfit with the --table flag. My >>> aparc_lh_thick_stats.txt contain entorhinal and parahippocampal >>> thickness values for 32 subjects. I ran the glm command and >>> received an error. Please, how can i solve this issue? I have >>> included my command, fsgd file, contrast matrix and error below. >>> Thanks >>> Best, >>> Paul >>> >>> GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex >>> --glmdir lh.thickness.glmdir >>> >>> >>> ERROR= "gdfRead(): reading age.fsgd >>> >>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >>> >>> Continuous Variable Means (all subjects) >>> >>> 0 Age 39.9375 17.3312 >>> >>> Class Means of each Continuous Variable >>> >>> 1 Group1 35.6316 >>> >>> 2 Group2 46.2308 >>> >>> INFO: gd2mtx_method is dods >>> >>> Reading source surface >>> /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white
>>> >>> Number of vertices 163842 >>> >>> Number of faces 327680 >>> >>> Total area 65416.984375 >>> >>> AvgVtxArea 0.399269 >>> >>> AvgVtxDist 0.721953 >>> >>> StdVtxDist 0.195470 >>> >>> >>> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ >>> >>> cwd /Users/MiracleOz/Documents/improvervsdeclinermri >>> >>> cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt--fsgd
>>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex >>> --glmdir lh.thickness.glmdir >>> >>> sysname Darwin >>> >>> hostname MacBook-Pro.local >>> >>> machine x86_64 >>> >>> user MiracleOz >>> >>> FixVertexAreaFlag = 1 >>> >>> UseMaskWithSmoothing 1 >>> >>> OneSampleGroupMean 0 >>> >>> y >>> /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
>>> >>> logyflag 0 >>> >>> usedti 0 >>> >>> FSGD age.fsgd >>> >>> labelmask >>> /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label
>>> >>> maskinv 0 >>> >>> glmdir lh.thickness.glmdir >>> >>> IllCondOK 0 >>> >>> ReScaleX 1 >>> >>> DoFFx 0 >>> >>> Creating output directory lh.thickness.glmdir >>> >>> Loading y from >>> /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
>>> >>> Found 66 data colums >>> >>> Found 0 data rows >>> >>> INFO: gd2mtx_method is dods >>> >>> Saving design matrix to lh.thickness.glmdir/Xg.dat >>> >>> Computing normalized matrix >>> >>> Normalized matrix condition is 32.2165 >>> >>> Matrix condition is 20734.7 >>> >>> Found 149955 points in label. >>> >>> ERROR: mri_reshape: number of elements cannot change >>> >>> nv1 = 163842, nv1 = 66 >>> >>> search space = 82219.962936 >>> >>> ERROR: dimension mismatch between y and X. >>> >>> y has 0 inputs, X has 32 rows." >>> >>> FSGD file: GroupDescriptorFile 1 >>> >>> Title MOT >>> >>> Class Group1 >>> >>> Class Group2 >>> >>> Variables Age >>> >>> Input 01053p Group1 23 >>> >>> Input 01054p Group1 43 >>> >>> Input 01061p Group2 39 >>> >>> Input 01062p Group2 19 >>> >>> Input 01074p Group2 28 >>> >>> .............. (I have more participants) >>> >>> >>> CONTRAST MATRIX: 1 -1 0 0 >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > _______________________________________________ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> The > information in this e-mail is intended only for the person to whom > it is addressed. If you believe this e-mail was sent to you in > error and the e-mail contains patient information, please contact > the Partners Compliance HelpLine at > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> . If the e-mail was sent > to you in error but does not contain patient information,please
> contact the sender and properly dispose of the e-mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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3:39 p.m.
I think that will work
On 04/19/2017 03:33 PM, miracle ozzoude wrote:
Hello Doug, Do you think writing the script with octave can substitute for matlab? I am using FS v6.0 and I have the annotval2surfoverlay.m. Thanks Best, Paul
On Wed, Apr 19, 2017 at 1:47 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, I don't have another solution for you. On 04/19/2017 01:42 PM, miracle ozzoude wrote: > Thanks Doug. However, I am running freesurfer analysis on my personal > computer and I don't have matlab. Also, I don't know how this matlab > script works/ matlab works. Any instructions on how to use it or > alternate? Please and thank you. > Best, > Paul. > > On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > It is a table of data, so you can't visualize it directly on anything. > You can try using annotval2surfoverlay.m to create a surface > overlay of > the data. > > > On 04/19/2017 10:05 AM, miracle ozzoude wrote: > > Hello Doug, > > It worked. The issue was due to formatting error with the aparc > file. > > Also, I was trying to visualize the result on the surface using > > freeview -f fsaverage/lh.pial -viewport 3d (clicking overlay on > > freeview and loading the sig.mgh). However, i got an error " > failed to > > display overlay". How can I visualize the result? Thanks > > Best, > > Paul > > > > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > You have a table of data, so no template is needed. If you > put the > > --surf before the --table, it probably runs, but it will ignore > > the surface > > > > > > On 4/18/17 9:58 PM, miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> wrote: > >> Thanks doug. Does it mean when using the --table flag, you > can't > >> use the fsaverage template? I came across several post in the > >> forum that used "--surf fsaverage lh " and it worked. > >> Best, > >> Paul > >> > >> Sent from my BlackBerry 10 smartphone. > >> *From: *Douglas Greve > >> *Sent: *Tuesday, April 18, 2017 9:52 PM > >> *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > >> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > >> *Reply To: *Freesurfer support list > >> *Subject: *Re: [Freesurfer] mri_glmfit error with aparc > table flag > >> > >> > >> Don't include --surf fsaverage lh. It thinks the input is a > >> surface, not a table > >> > >> > >> > >> On 4/18/17 9:21 PM, miracle ozzoude wrote: > >>> Hello freesurfer, > >>> I am trying to run mri_glmfit with the --table flag. My > >>> aparc_lh_thick_stats.txt contain entorhinal and > parahippocampal > >>> thickness values for 32 subjects. I ran the glm command and > >>> received an error. Please, how can i solve this issue? I have > >>> included my command, fsgd file, contrast matrix and error > below. > >>> Thanks > >>> Best, > >>> Paul > >>> > >>> GLM command: mri_glmfit --table aparc_lh_thick_stats.txt > --fsgd > >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh > --cortex > >>> --glmdir lh.thickness.glmdir > >>> > >>> > >>> ERROR= "gdfRead(): reading age.fsgd > >>> > >>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be > done. > >>> > >>> Continuous Variable Means (all subjects) > >>> > >>> 0 Age 39.9375 17.3312 > >>> > >>> Class Means of each Continuous Variable > >>> > >>> 1 Group1 35.6316 > >>> > >>> 2 Group2 46.2308 > >>> > >>> INFO: gd2mtx_method is dods > >>> > >>> Reading source surface > >>> > /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white > >>> > >>> Number of vertices 163842 > >>> > >>> Number of faces 327680 > >>> > >>> Total area 65416.984375 > >>> > >>> AvgVtxArea 0.399269 > >>> > >>> AvgVtxDist 0.721953 > >>> > >>> StdVtxDist 0.195470 > >>> > >>> > >>> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman > Exp $ > >>> > >>> cwd /Users/MiracleOz/Documents/improvervsdeclinermri > >>> > >>> cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd > >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh > --cortex > >>> --glmdir lh.thickness.glmdir > >>> > >>> sysname Darwin > >>> > >>> hostname MacBook-Pro.local > >>> > >>> machine x86_64 > >>> > >>> user MiracleOz > >>> > >>> FixVertexAreaFlag = 1 > >>> > >>> UseMaskWithSmoothing 1 > >>> > >>> OneSampleGroupMean 0 > >>> > >>> y > >>> > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt > >>> > >>> logyflag 0 > >>> > >>> usedti 0 > >>> > >>> FSGD age.fsgd > >>> > >>> labelmask > >>> > /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label > >>> > >>> maskinv 0 > >>> > >>> glmdir lh.thickness.glmdir > >>> > >>> IllCondOK 0 > >>> > >>> ReScaleX 1 > >>> > >>> DoFFx 0 > >>> > >>> Creating output directory lh.thickness.glmdir > >>> > >>> Loading y from > >>> > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt > >>> > >>> Found 66 data colums > >>> > >>> Found 0 data rows > >>> > >>> INFO: gd2mtx_method is dods > >>> > >>> Saving design matrix to lh.thickness.glmdir/Xg.dat > >>> > >>> Computing normalized matrix > >>> > >>> Normalized matrix condition is 32.2165 > >>> > >>> Matrix condition is 20734.7 > >>> > >>> Found 149955 points in label. > >>> > >>> ERROR: mri_reshape: number of elements cannot change > >>> > >>> nv1 = 163842, nv1 = 66 > >>> > >>> search space = 82219.962936 > >>> > >>> ERROR: dimension mismatch between y and X. > >>> > >>> y has 0 inputs, X has 32 rows." > >>> > >>> FSGD file: GroupDescriptorFile 1 > >>> > >>> Title MOT > >>> > >>> Class Group1 > >>> > >>> Class Group2 > >>> > >>> Variables Age > >>> > >>> Input 01053p Group1 23 > >>> > >>> Input 01054p Group1 43 > >>> > >>> Input 01061p Group2 39 > >>> > >>> Input 01062p Group2 19 > >>> > >>> Input 01074p Group2 28 > >>> > >>> .............. (I have more participants) > >>> > >>> > >>> CONTRAST MATRIX: 1 -1 0 0 > >>> > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > _______________________________________________ Freesurfer > mailing > > list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> The > > information in this e-mail is intended only for the person > to whom > > it is addressed. If you believe this e-mail was sent to you in > > error and the e-mail contains patient information, please > contact > > the Partners Compliance HelpLine at > > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> . If the e-mail was sent > > to you in error but does not contain patient information, please > > contact the sender and properly dispose of the e-mail. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > -- > Douglas N. 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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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20 Apr
20 Apr
10:10 a.m.
Hello Doug, I downloaded and installed octave. However, I can't find the annotval2surfoverlay.m file in the matlab directory of freesurfer. Does it come with FS v6 or do i need to download the file? Also, I was looking into the annotval2surfoverlay file and I have couple of questions. % Run these commands in matlab % annotnames = strvcat('superiortemporal','insula','postcentral'); % annotvals = [1.1 2.2 3.7]; % annotfile = '~/subjects/fsaverage/label/lh.aparc.annot'; % surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile); % clear mri % mri.vol = surfoverlay; % MRIwrite(mri,'vals.mgh'); % 1) Are the annotation values (annotvals) from results after correcting for multiple comparisons using mri_fdr? 2) Do I need to add octave path to freesurfer PATH like the example below?
setenv FS_USE_OCTAVE 4.0.3
setenv FS_OCTAVE_LIB /Applications/octave/lib setenv FS_OCTAVE_BIN /Application/octave/binary
On Wed, Apr 19, 2017 at 3:39 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
I think that will work
On 04/19/2017 03:33 PM, miracle ozzoude wrote:
Hello Doug, Do you think writing the script with octave can substitute for matlab? I am using FS v6.0 and I have the annotval2surfoverlay.m. Thanks Best, Paul
On Wed, Apr 19, 2017 at 1:47 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, I don't have another solution for you. On 04/19/2017 01:42 PM, miracle ozzoude wrote: > Thanks Doug. However, I am running freesurfer analysis on my personal > computer and I don't have matlab. Also, I don't know how thismatlab
> script works/ matlab works. Any instructions on how to use it or > alternate? Please and thank you. > Best, > Paul. > > On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > It is a table of data, so you can't visualize it directly on anything. > You can try using annotval2surfoverlay.m to create a surface > overlay of > the data. > > > On 04/19/2017 10:05 AM, miracle ozzoude wrote: > > Hello Doug, > > It worked. The issue was due to formatting error with the aparc > file. > > Also, I was trying to visualize the result on the surface using > > freeview -f fsaverage/lh.pial -viewport 3d (clicking overlay on > > freeview and loading the sig.mgh). However, i got an error " > failed to > > display overlay". How can I visualize the result? Thanks > > Best, > > Paul > > > > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:
> > > > You have a table of data, so no template is needed. Ifyou
> put the > > --surf before the --table, it probably runs, but it will ignore > > the surface > > > > > > On 4/18/17 9:58 PM, miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>
<mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> wrote: > >> Thanks doug. Does it mean when using the --table flag, you > can't > >> use the fsaverage template? I came across several post in the > >> forum that used "--surf fsaverage lh " and it worked. > >> Best, > >> Paul > >> > >> Sent from my BlackBerry 10 smartphone. > >> *From: *Douglas Greve > >> *Sent: *Tuesday, April 18, 2017 9:52 PM > >> *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > >> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > >> *Reply To: *Freesurfer support list > >> *Subject: *Re: [Freesurfer] mri_glmfit error with aparc > table flag > >> > >> > >> Don't include --surf fsaverage lh. It thinks the input is a > >> surface, not a table > >> > >> > >> > >> On 4/18/17 9:21 PM, miracle ozzoude wrote: > >>> Hello freesurfer, > >>> I am trying to run mri_glmfit with the --table flag. My > >>> aparc_lh_thick_stats.txt contain entorhinal and > parahippocampal > >>> thickness values for 32 subjects. I ran the glm command and > >>> received an error. Please, how can i solve this issue? I have > >>> included my command, fsgd file, contrast matrix and error > below. > >>> Thanks > >>> Best, > >>> Paul > >>> > >>> GLM command: mri_glmfit --tableaparc_lh_thick_stats.txt
> --fsgd > >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh > --cortex > >>> --glmdir lh.thickness.glmdir > >>> > >>> > >>> ERROR= "gdfRead(): reading age.fsgd > >>> > >>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be > done. > >>> > >>> Continuous Variable Means (all subjects) > >>> > >>> 0 Age 39.9375 17.3312 > >>> > >>> Class Means of each Continuous Variable > >>> > >>> 1 Group1 35.6316 > >>> > >>> 2 Group2 46.2308 > >>> > >>> INFO: gd2mtx_method is dods > >>> > >>> Reading source surface > >>> > /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white
> >>> > >>> Number of vertices 163842 > >>> > >>> Number of faces 327680 > >>> > >>> Total area 65416.984375 > >>> > >>> AvgVtxArea 0.399269 > >>> > >>> AvgVtxDist 0.721953 > >>> > >>> StdVtxDist 0.195470 > >>> > >>> > >>> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman > Exp $ > >>> > >>> cwd /Users/MiracleOz/Documents/improvervsdeclinermri > >>> > >>> cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd > >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh > --cortex > >>> --glmdir lh.thickness.glmdir > >>> > >>> sysname Darwin > >>> > >>> hostname MacBook-Pro.local > >>> > >>> machine x86_64 > >>> > >>> user MiracleOz > >>> > >>> FixVertexAreaFlag = 1 > >>> > >>> UseMaskWithSmoothing 1 > >>> > >>> OneSampleGroupMean 0 > >>> > >>> y > >>> > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
> >>> > >>> logyflag 0 > >>> > >>> usedti 0 > >>> > >>> FSGD age.fsgd > >>> > >>> labelmask > >>> > /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label
> >>> > >>> maskinv 0 > >>> > >>> glmdir lh.thickness.glmdir > >>> > >>> IllCondOK 0 > >>> > >>> ReScaleX 1 > >>> > >>> DoFFx 0 > >>> > >>> Creating output directory lh.thickness.glmdir > >>> > >>> Loading y from > >>> > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
> >>> > >>> Found 66 data colums > >>> > >>> Found 0 data rows > >>> > >>> INFO: gd2mtx_method is dods > >>> > >>> Saving design matrix to lh.thickness.glmdir/Xg.dat > >>> > >>> Computing normalized matrix > >>> > >>> Normalized matrix condition is 32.2165 > >>> > >>> Matrix condition is 20734.7 > >>> > >>> Found 149955 points in label. > >>> > >>> ERROR: mri_reshape: number of elements cannot change > >>> > >>> nv1 = 163842, nv1 = 66 > >>> > >>> search space = 82219.962936 > >>> > >>> ERROR: dimension mismatch between y and X. > >>> > >>> y has 0 inputs, X has 32 rows." > >>> > >>> FSGD file: GroupDescriptorFile 1 > >>> > >>> Title MOT > >>> > >>> Class Group1 > >>> > >>> Class Group2 > >>> > >>> Variables Age > >>> > >>> Input 01053p Group1 23 > >>> > >>> Input 01054p Group1 43 > >>> > >>> Input 01061p Group2 39 > >>> > >>> Input 01062p Group2 19 > >>> > >>> Input 01074p Group2 28 > >>> > >>> .............. (I have more participants) > >>> > >>> > >>> CONTRAST MATRIX: 1 -1 0 0 > >>> > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > _______________________________________________Freesurfer
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<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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10:55 a.m.
you can get it here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
On 04/20/2017 10:10 AM, miracle ozzoude wrote:
Hello Doug, I downloaded and installed octave. However, I can't find the annotval2surfoverlay.m file in the matlab directory of freesurfer. Does it come with FS v6 or do i need to download the file? Also, I was looking into the annotval2surfoverlay file and I have couple of questions. % Run these commands in matlab % annotnames = strvcat('superiortemporal','insula','postcentral'); % annotvals = [1.1 2.2 3.7]; % annotfile = '~/subjects/fsaverage/label/lh.aparc.annot'; % surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile); % clear mri % mri.vol = surfoverlay; % MRIwrite(mri,'vals.mgh'); %
- Are the annotation values (annotvals) from results after correcting
for multiple comparisons using mri_fdr? 2) Do I need to add octave path to freesurfer PATH like the example below? setenv FS_USE_OCTAVE 4.0.3
setenv FS_OCTAVE_LIB /Applications/octave/lib setenv FS_OCTAVE_BIN /Application/octave/binary
On Wed, Apr 19, 2017 at 3:39 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think that will work On 04/19/2017 03:33 PM, miracle ozzoude wrote: > Hello Doug, > Do you think writing the script with octave can substitute for matlab? > I am using FS v6.0 and I have the annotval2surfoverlay.m. Thanks > Best, > Paul > > On Wed, Apr 19, 2017 at 1:47 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Sorry, I don't have another solution for you. > > > On 04/19/2017 01:42 PM, miracle ozzoude wrote: > > Thanks Doug. However, I am running freesurfer analysis on my > personal > > computer and I don't have matlab. Also, I don't know how this matlab > > script works/ matlab works. Any instructions on how to use it or > > alternate? Please and thank you. > > Best, > > Paul. > > > > On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > It is a table of data, so you can't visualize it directly on > anything. > > You can try using annotval2surfoverlay.m to create a surface > > overlay of > > the data. > > > > > > On 04/19/2017 10:05 AM, miracle ozzoude wrote: > > > Hello Doug, > > > It worked. The issue was due to formatting error with the > aparc > > file. > > > Also, I was trying to visualize the result on the surface > using > > > freeview -f fsaverage/lh.pial -viewport 3d (clicking > overlay on > > > freeview and loading the sig.mgh). However, i got an error " > > failed to > > > display overlay". How can I visualize the result? Thanks > > > Best, > > > Paul > > > > > > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve > > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > > > You have a table of data, so no template is needed. If you > > put the > > > --surf before the --table, it probably runs, but it > will ignore > > > the surface > > > > > > > > > On 4/18/17 9:58 PM, miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> wrote: > > >> Thanks doug. Does it mean when using the --table > flag, you > > can't > > >> use the fsaverage template? I came across several > post in the > > >> forum that used "--surf fsaverage lh " and it worked. > > >> Best, > > >> Paul > > >> > > >> Sent from my BlackBerry 10 smartphone. > > >> *From: *Douglas Greve > > >> *Sent: *Tuesday, April 18, 2017 9:52 PM > > >> *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > >> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > >> *Reply To: *Freesurfer support list > > >> *Subject: *Re: [Freesurfer] mri_glmfit error with aparc > > table flag > > >> > > >> > > >> Don't include --surf fsaverage lh. It thinks the > input is a > > >> surface, not a table > > >> > > >> > > >> > > >> On 4/18/17 9:21 PM, miracle ozzoude wrote: > > >>> Hello freesurfer, > > >>> I am trying to run mri_glmfit with the --table flag. My > > >>> aparc_lh_thick_stats.txt contain entorhinal and > > parahippocampal > > >>> thickness values for 32 subjects. I ran the glm > command and > > >>> received an error. Please, how can i solve this > issue? I have > > >>> included my command, fsgd file, contrast matrix and > error > > below. > > >>> Thanks > > >>> Best, > > >>> Paul > > >>> > > >>> GLM command: mri_glmfit --table aparc_lh_thick_stats.txt > > --fsgd > > >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh > > --cortex > > >>> --glmdir lh.thickness.glmdir > > >>> > > >>> > > >>> ERROR= "gdfRead(): reading age.fsgd > > >>> > > >>> INFO: DeMeanFlag keyword not found, DeMeaning will > NOT be > > done. > > >>> > > >>> Continuous Variable Means (all subjects) > > >>> > > >>> 0 Age 39.9375 17.3312 > > >>> > > >>> Class Means of each Continuous Variable > > >>> > > >>> 1 Group1 35.6316 > > >>> > > >>> 2 Group2 46.2308 > > >>> > > >>> INFO: gd2mtx_method is dods > > >>> > > >>> Reading source surface > > >>> > > > /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white > > >>> > > >>> Number of vertices 163842 > > >>> > > >>> Number of faces 327680 > > >>> > > >>> Total area 65416.984375 > > >>> > > >>> AvgVtxArea 0.399269 > > >>> > > >>> AvgVtxDist 0.721953 > > >>> > > >>> StdVtxDist 0.195470 > > >>> > > >>> > > >>> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 > zkaufman > > Exp $ > > >>> > > >>> cwd /Users/MiracleOz/Documents/improvervsdeclinermri > > >>> > > >>> cmdline mri_glmfit.bin --table > aparc_lh_thick_stats.txt --fsgd > > >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh > > --cortex > > >>> --glmdir lh.thickness.glmdir > > >>> > > >>> sysname Darwin > > >>> > > >>> hostname MacBook-Pro.local > > >>> > > >>> machine x86_64 > > >>> > > >>> user MiracleOz > > >>> > > >>> FixVertexAreaFlag = 1 > > >>> > > >>> UseMaskWithSmoothing 1 > > >>> > > >>> OneSampleGroupMean 0 > > >>> > > >>> y > > >>> > > > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt > > >>> > > >>> logyflag 0 > > >>> > > >>> usedti 0 > > >>> > > >>> FSGD age.fsgd > > >>> > > >>> labelmask > > >>> > > > /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label > > >>> > > >>> maskinv 0 > > >>> > > >>> glmdir lh.thickness.glmdir > > >>> > > >>> IllCondOK 0 > > >>> > > >>> ReScaleX 1 > > >>> > > >>> DoFFx 0 > > >>> > > >>> Creating output directory lh.thickness.glmdir > > >>> > > >>> Loading y from > > >>> > > > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt > > >>> > > >>> Found 66 data colums > > >>> > > >>> Found 0 data rows > > >>> > > >>> INFO: gd2mtx_method is dods > > >>> > > >>> Saving design matrix to lh.thickness.glmdir/Xg.dat > > >>> > > >>> Computing normalized matrix > > >>> > > >>> Normalized matrix condition is 32.2165 > > >>> > > >>> Matrix condition is 20734.7 > > >>> > > >>> Found 149955 points in label. > > >>> > > >>> ERROR: mri_reshape: number of elements cannot change > > >>> > > >>> nv1 = 163842, nv1 = 66 > > >>> > > >>> search space = 82219.962936 > > >>> > > >>> ERROR: dimension mismatch between y and X. > > >>> > > >>> y has 0 inputs, X has 32 rows." > > >>> > > >>> FSGD file: GroupDescriptorFile 1 > > >>> > > >>> Title MOT > > >>> > > >>> Class Group1 > > >>> > > >>> Class Group2 > > >>> > > >>> Variables Age > > >>> > > >>> Input 01053p Group1 23 > > >>> > > >>> Input 01054p Group1 43 > > >>> > > >>> Input 01061p Group2 39 > > >>> > > >>> Input 01062p Group2 19 > > >>> > > >>> Input 01074p Group2 28 > > >>> > > >>> .............. (I have more participants) > > >>> > > >>> > > >>> CONTRAST MATRIX: 1 -1 0 0 > > >>> > > >>> > > >>> > > >>> _______________________________________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > 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<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> The > > > information in this e-mail is intended only for the person > > to whom > > > it is addressed. If you believe this e-mail was sent > to you in > > > error and the e-mail contains patient information, please > > contact > > > the Partners Compliance HelpLine at > > > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> > > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>>> . If the e-mail was sent > > > to you in error but does not contain patient > information, please > > > contact the sender and properly dispose of the e-mail. > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
11:08 a.m.
Thank very much Doug. Also, I was looking into the annotval2surfoverlay file and I have couple of questions. % Run these commands in matlab % annotnames = strvcat('superiortemporal','insula','postcentral'); % annotvals = [1.1 2.2 3.7]; % annotfile = '~/paul_analysis/fsaverage/label/lh.aparc.annot'; % surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile); % clear mri % mri.vol = surfoverlay; % MRIwrite(mri,'vals.mgh'); % 1) Correct me if I am wrong, the annotation values (annotvals) are from results after correcting for multiple comparisons using mri_fdr? 2) Is this correct way to add octave path to freesurfer's path?
setenv FS_USE_OCTAVE 4.0.3
setenv FS_OCTAVE_LIB /Applications/octave/lib setenv FS_OCTAVE_BIN /Application/octave/binary
Thanks,
Best,
Paul
On Thu, Apr 20, 2017 at 10:55 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
you can get it here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
On 04/20/2017 10:10 AM, miracle ozzoude wrote:
Hello Doug, I downloaded and installed octave. However, I can't find the annotval2surfoverlay.m file in the matlab directory of freesurfer. Does it come with FS v6 or do i need to download the file? Also, I was looking into the annotval2surfoverlay file and I have couple of questions. % Run these commands in matlab % annotnames = strvcat('superiortemporal','insula','postcentral'); % annotvals = [1.1 2.2 3.7]; % annotfile = '~/subjects/fsaverage/label/lh.aparc.annot'; % surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile); % clear mri % mri.vol = surfoverlay; % MRIwrite(mri,'vals.mgh'); %
- Are the annotation values (annotvals) from results after correcting
for multiple comparisons using mri_fdr? 2) Do I need to add octave path to freesurfer PATH like the example below? setenv FS_USE_OCTAVE 4.0.3
setenv FS_OCTAVE_LIB /Applications/octave/lib setenv FS_OCTAVE_BIN /Application/octave/binary
On Wed, Apr 19, 2017 at 3:39 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think that will work On 04/19/2017 03:33 PM, miracle ozzoude wrote: > Hello Doug, > Do you think writing the script with octave can substitute for matlab? > I am using FS v6.0 and I have the annotval2surfoverlay.m. Thanks > Best, > Paul > > On Wed, Apr 19, 2017 at 1:47 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Sorry, I don't have another solution for you. > > > On 04/19/2017 01:42 PM, miracle ozzoude wrote: > > Thanks Doug. However, I am running freesurfer analysis on my > personal > > computer and I don't have matlab. Also, I don't know how this matlab > > script works/ matlab works. Any instructions on how to use it or > > alternate? Please and thank you. > > Best, > > Paul. > > > > On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > It is a table of data, so you can't visualize it directly on > anything. > > You can try using annotval2surfoverlay.m to create a surface > > overlay of > > the data. > > > > > > On 04/19/2017 10:05 AM, miracle ozzoude wrote: > > > Hello Doug, > > > It worked. The issue was due to formatting error with the > aparc > > file. > > > Also, I was trying to visualize the result on the surface > using > > > freeview -f fsaverage/lh.pial -viewport 3d (clicking > overlay on > > > freeview and loading the sig.mgh). However, i got an error " > > failed to > > > display overlay". How can I visualize the result?Thanks
> > > Best, > > > Paul > > > > > > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve > > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > > > You have a table of data, so no template is needed. If you > > put the > > > --surf before the --table, it probably runs, but it > will ignore > > > the surface > > > > > > > > > On 4/18/17 9:58 PM, miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> wrote: > > >> Thanks doug. Does it mean when using the --table > flag, you > > can't > > >> use the fsaverage template? I came across several > post in the > > >> forum that used "--surf fsaverage lh " and it worked. > > >> Best, > > >> Paul > > >> > > >> Sent from my BlackBerry 10 smartphone. > > >> *From: *Douglas Greve > > >> *Sent: *Tuesday, April 18, 2017 9:52 PM > > >> *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > >> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > >> *Reply To: *Freesurfer support list > > >> *Subject: *Re: [Freesurfer] mri_glmfit error with aparc > > table flag > > >> > > >> > > >> Don't include --surf fsaverage lh. It thinks the > input is a > > >> surface, not a table > > >> > > >> > > >> > > >> On 4/18/17 9:21 PM, miracle ozzoude wrote: > > >>> Hello freesurfer, > > >>> I am trying to run mri_glmfit with the --table flag. My > > >>> aparc_lh_thick_stats.txt contain entorhinal and > > parahippocampal > > >>> thickness values for 32 subjects. I ran the glm > command and > > >>> received an error. Please, how can i solve this > issue? I have > > >>> included my command, fsgd file, contrast matrix and > error > > below. > > >>> Thanks > > >>> Best, > > >>> Paul > > >>> > > >>> GLM command: mri_glmfit --table aparc_lh_thick_stats.txt > > --fsgd > > >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh > > --cortex > > >>> --glmdir lh.thickness.glmdir > > >>> > > >>> > > >>> ERROR= "gdfRead(): reading age.fsgd > > >>> > > >>> INFO: DeMeanFlag keyword not found, DeMeaningwill
> NOT be > > done. > > >>> > > >>> Continuous Variable Means (all subjects) > > >>> > > >>> 0 Age 39.9375 17.3312 > > >>> > > >>> Class Means of each Continuous Variable > > >>> > > >>> 1 Group1 35.6316 > > >>> > > >>> 2 Group2 46.2308 > > >>> > > >>> INFO: gd2mtx_method is dods > > >>> > > >>> Reading source surface > > >>> > > > /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white
> > >>> > > >>> Number of vertices 163842 > > >>> > > >>> Number of faces 327680 > > >>> > > >>> Total area 65416.984375 > > >>> > > >>> AvgVtxArea 0.399269 > > >>> > > >>> AvgVtxDist 0.721953 > > >>> > > >>> StdVtxDist 0.195470 > > >>> > > >>> > > >>> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 > zkaufman > > Exp $ > > >>> > > >>> cwd /Users/MiracleOz/Documents/improvervsdeclinermri > > >>> > > >>> cmdline mri_glmfit.bin --table > aparc_lh_thick_stats.txt --fsgd > > >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh > > --cortex > > >>> --glmdir lh.thickness.glmdir > > >>> > > >>> sysname Darwin > > >>> > > >>> hostname MacBook-Pro.local > > >>> > > >>> machine x86_64 > > >>> > > >>> user MiracleOz > > >>> > > >>> FixVertexAreaFlag = 1 > > >>> > > >>> UseMaskWithSmoothing 1 > > >>> > > >>> OneSampleGroupMean 0 > > >>> > > >>> y > > >>> > > > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
> > >>> > > >>> logyflag 0 > > >>> > > >>> usedti 0 > > >>> > > >>> FSGD age.fsgd > > >>> > > >>> labelmask > > >>> > > > /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label
> > >>> > > >>> maskinv 0 > > >>> > > >>> glmdir lh.thickness.glmdir > > >>> > > >>> IllCondOK 0 > > >>> > > >>> ReScaleX 1 > > >>> > > >>> DoFFx 0 > > >>> > > >>> Creating output directory lh.thickness.glmdir > > >>> > > >>> Loading y from > > >>> > > > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
> > >>> > > >>> Found 66 data colums > > >>> > > >>> Found 0 data rows > > >>> > > >>> INFO: gd2mtx_method is dods > > >>> > > >>> Saving design matrix tolh.thickness.glmdir/Xg.dat
> > >>> > > >>> Computing normalized matrix > > >>> > > >>> Normalized matrix condition is 32.2165 > > >>> > > >>> Matrix condition is 20734.7 > > >>> > > >>> Found 149955 points in label. > > >>> > > >>> ERROR: mri_reshape: number of elements cannot change > > >>> > > >>> nv1 = 163842, nv1 = 66 > > >>> > > >>> search space = 82219.962936 > > >>> > > >>> ERROR: dimension mismatch between y and X. > > >>> > > >>> y has 0 inputs, X has 32 rows." > > >>> > > >>> FSGD file: GroupDescriptorFile 1 > > >>> > > >>> Title MOT > > >>> > > >>> Class Group1 > > >>> > > >>> Class Group2 > > >>> > > >>> Variables Age > > >>> > > >>> Input 01053p Group1 23 > > >>> > > >>> Input 01054p Group1 43 > > >>> > > >>> Input 01061p Group2 39 > > >>> > > >>> Input 01062p Group2 19 > > >>> > > >>> Input 01074p Group2 28 > > >>> > > >>> .............. (I have more participants) > > >>> > > >>> > > >>> CONTRAST MATRIX: 1 -1 0 0 > > >>> > > >>> > > >>> > > >>> _______________________________________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > 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> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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11:16 a.m.
On 04/20/2017 11:08 AM, miracle ozzoude wrote:
Thank very much Doug. Also, I was looking into the annotval2surfoverlay file and I have couple of questions. % Run these commands in matlab % annotnames = strvcat('superiortemporal','insula','postcentral'); % annotvals = [1.1 2.2 3.7]; % annotfile = '~/paul_analysis/fsaverage/label/lh.aparc.annot'; % surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile); % clear mri % mri.vol = surfoverlay; % MRIwrite(mri,'vals.mgh'); %
- Correct me if I am wrong, the annotation values (annotvals) are
from results after correcting for multiple comparisons using mri_fdr?
They can be anything that you have one value per annotation.
- Is this correct way to add octave path to freesurfer's path?
Sorry, I have no idea
setenv FS_USE_OCTAVE 4.0.3
setenv FS_OCTAVE_LIB /Applications/octave/lib setenv FS_OCTAVE_BIN /Application/octave/binary Thanks, Best, Paul
On Thu, Apr 20, 2017 at 10:55 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
you can get it here https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m <https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m> On 04/20/2017 10:10 AM, miracle ozzoude wrote: > Hello Doug, > I downloaded and installed octave. However, I can't find the > annotval2surfoverlay.m file in the matlab directory of freesurfer. > Does it come with FS v6 or do i need to download the file? Also, I was > looking into the annotval2surfoverlay file and I have couple of > questions. > % Run these commands in matlab > % annotnames = strvcat('superiortemporal','insula','postcentral'); > % annotvals = [1.1 2.2 3.7]; > % annotfile = '~/subjects/fsaverage/label/lh.aparc.annot'; > % surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile); > % clear mri > % mri.vol = surfoverlay; > % MRIwrite(mri,'vals.mgh'); > % > 1) Are the annotation values (annotvals) from results after correcting > for multiple comparisons using mri_fdr? > 2) Do I need to add octave path to freesurfer PATH like the example > below? > setenv FS_USE_OCTAVE 4.0.3 > > setenv FS_OCTAVE_LIB /Applications/octave/lib > setenv FS_OCTAVE_BIN /Application/octave/binary > > On Wed, Apr 19, 2017 at 3:39 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > I think that will work > > > On 04/19/2017 03:33 PM, miracle ozzoude wrote: > > Hello Doug, > > Do you think writing the script with octave can substitute for > matlab? > > I am using FS v6.0 and I have the annotval2surfoverlay.m. Thanks > > Best, > > Paul > > > > On Wed, Apr 19, 2017 at 1:47 PM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > Sorry, I don't have another solution for you. > > > > > > On 04/19/2017 01:42 PM, miracle ozzoude wrote: > > > Thanks Doug. However, I am running freesurfer analysis on my > > personal > > > computer and I don't have matlab. Also, I don't know how > this matlab > > > script works/ matlab works. Any instructions on how to use > it or > > > alternate? Please and thank you. > > > Best, > > > Paul. > > > > > > On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve > > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > > > It is a table of data, so you can't visualize it > directly on > > anything. > > > You can try using annotval2surfoverlay.m to create a > surface > > > overlay of > > > the data. > > > > > > > > > On 04/19/2017 10:05 AM, miracle ozzoude wrote: > > > > Hello Doug, > > > > It worked. The issue was due to formatting error > with the > > aparc > > > file. > > > > Also, I was trying to visualize the result on the > surface > > using > > > > freeview -f fsaverage/lh.pial -viewport 3d (clicking > > overlay on > > > > freeview and loading the sig.mgh). However, i got an > error " > > > failed to > > > > display overlay". How can I visualize the result? Thanks > > > > Best, > > > > Paul > > > > > > > > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve > > > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>> wrote: > > > > > > > > You have a table of data, so no template is > needed. If you > > > put the > > > > --surf before the --table, it probably runs, but it > > will ignore > > > > the surface > > > > > > > > > > > > On 4/18/17 9:58 PM, miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> > > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>> wrote: > > > >> Thanks doug. Does it mean when using the --table > > flag, you > > > can't > > > >> use the fsaverage template? I came across several > > post in the > > > >> forum that used "--surf fsaverage lh " and it > worked. > > > >> Best, > > > >> Paul > > > >> > > > >> Sent from my BlackBerry 10 smartphone. > > > >> *From: *Douglas Greve > > > >> *Sent: *Tuesday, April 18, 2017 9:52 PM > > > >> *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > >> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > > > >> *Reply To: *Freesurfer support list > > > >> *Subject: *Re: [Freesurfer] mri_glmfit error > with aparc > > > table flag > > > >> > > > >> > > > >> Don't include --surf fsaverage lh. It thinks the > > input is a > > > >> surface, not a table > > > >> > > > >> > > > >> > > > >> On 4/18/17 9:21 PM, miracle ozzoude wrote: > > > >>> Hello freesurfer, > > > >>> I am trying to run mri_glmfit with the --table > flag. My > > > >>> aparc_lh_thick_stats.txt contain entorhinal and > > > parahippocampal > > > >>> thickness values for 32 subjects. I ran the glm > > command and > > > >>> received an error. Please, how can i solve this > > issue? I have > > > >>> included my command, fsgd file, contrast > matrix and > > error > > > below. > > > >>> Thanks > > > >>> Best, > > > >>> Paul > > > >>> > > > >>> GLM command: mri_glmfit --table > aparc_lh_thick_stats.txt > > > --fsgd > > > >>> age.fsgd --C age1.mtx --C age2.mtx --surf > fsaverage lh > > > --cortex > > > >>> --glmdir lh.thickness.glmdir > > > >>> > > > >>> > > > >>> ERROR= "gdfRead(): reading age.fsgd > > > >>> > > > >>> INFO: DeMeanFlag keyword not found, DeMeaning will > > NOT be > > > done. > > > >>> > > > >>> Continuous Variable Means (all subjects) > > > >>> > > > >>> 0 Age 39.9375 17.3312 > > > >>> > > > >>> Class Means of each Continuous Variable > > > >>> > > > >>> 1 Group1 35.6316 > > > >>> > > > >>> 2 Group2 46.2308 > > > >>> > > > >>> INFO: gd2mtx_method is dods > > > >>> > > > >>> Reading source surface > > > >>> > > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white > > > >>> > > > >>> Number of vertices 163842 > > > >>> > > > >>> Number of faces 327680 > > > >>> > > > >>> Total area 65416.984375 > > > >>> > > > >>> AvgVtxArea 0.399269 > > > >>> > > > >>> AvgVtxDist 0.721953 > > > >>> > > > >>> StdVtxDist 0.195470 > > > >>> > > > >>> > > > >>> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 > > zkaufman > > > Exp $ > > > >>> > > > >>> cwd > /Users/MiracleOz/Documents/improvervsdeclinermri > > > >>> > > > >>> cmdline mri_glmfit.bin --table > > aparc_lh_thick_stats.txt --fsgd > > > >>> age.fsgd --C age1.mtx --C age2.mtx --surf > fsaverage lh > > > --cortex > > > >>> --glmdir lh.thickness.glmdir > > > >>> > > > >>> sysname Darwin > > > >>> > > > >>> hostname MacBook-Pro.local > > > >>> > > > >>> machine x86_64 > > > >>> > > > >>> user MiracleOz > > > >>> > > > >>> FixVertexAreaFlag = 1 > > > >>> > > > >>> UseMaskWithSmoothing 1 > > > >>> > > > >>> OneSampleGroupMean 0 > > > >>> > > > >>> y > > > >>> > > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt > > > >>> > > > >>> logyflag 0 > > > >>> > > > >>> usedti 0 > > > >>> > > > >>> FSGD age.fsgd > > > >>> > > > >>> labelmask > > > >>> > > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label > > > >>> > > > >>> maskinv 0 > > > >>> > > > >>> glmdir lh.thickness.glmdir > > > >>> > > > >>> IllCondOK 0 > > > >>> > > > >>> ReScaleX 1 > > > >>> > > > >>> DoFFx 0 > > > >>> > > > >>> Creating output directory lh.thickness.glmdir > > > >>> > > > >>> Loading y from > > > >>> > > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt > > > >>> > > > >>> Found 66 data colums > > > >>> > > > >>> Found 0 data rows > > > >>> > > > >>> INFO: gd2mtx_method is dods > > > >>> > > > >>> Saving design matrix to lh.thickness.glmdir/Xg.dat > > > >>> > > > >>> Computing normalized matrix > > > >>> > > > >>> Normalized matrix condition is 32.2165 > > > >>> > > > >>> Matrix condition is 20734.7 > > > >>> > > > >>> Found 149955 points in label. > > > >>> > > > >>> ERROR: mri_reshape: number of elements cannot > change > > > >>> > > > >>> nv1 = 163842, nv1 = 66 > > > >>> > > > >>> search space = 82219.962936 > > > >>> > > > >>> ERROR: dimension mismatch between y and X. > > > >>> > > > >>> y has 0 inputs, X has 32 rows." > > > >>> > > > >>> FSGD file: GroupDescriptorFile 1 > > > >>> > > > >>> Title MOT > > > >>> > > > >>> Class Group1 > > > >>> > > > >>> Class Group2 > > > >>> > > > >>> Variables Age > > > >>> > > > >>> Input 01053p Group1 23 > > > >>> > > > >>> Input 01054p Group1 43 > > > >>> > > > >>> Input 01061p Group2 39 > > > >>> > > > >>> Input 01062p Group2 19 > > > >>> > > > >>> Input 01074p Group2 28 > > > >>> > > > >>> .............. (I have more participants) > > > >>> > > > >>> > > > >>> CONTRAST MATRIX: 1 -1 0 0 > > > >>> > > > >>> > > > >>> > > > >>> _______________________________________________ > > > >>> Freesurfer mailing list > > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > >>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>>> > > > >> > > > >> _______________________________________________ > > > >> Freesurfer mailing list > > > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > >> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>>> > > > > _______________________________________________ > Freesurfer > > > mailing > > > > list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>>> The > > > > information in this e-mail is intended only for > the person > > > to whom > > > > it is addressed. If you believe this e-mail was sent > > to you in > > > > error and the e-mail contains patient > information, please > > > contact > > > > the Partners Compliance HelpLine at > > > > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> > > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>>> > > > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> > > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>>>> . If the e-mail was sent > > > > to you in error but does not contain patient > > information, please > > > > contact the sender and properly dispose of the > e-mail. > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>> > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>>> > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>> > > > Outgoing: > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>>> > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > -- > > Douglas N. 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Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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21 Apr
21 Apr
1:54 p.m.
Hello Doug, Should I put the annotval2surfoverlay.m file in the matlab subfolder or freesurfer? Best, Paul
On Thu, Apr 20, 2017 at 11:16 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
On 04/20/2017 11:08 AM, miracle ozzoude wrote:
Thank very much Doug. Also, I was looking into the annotval2surfoverlay file and I have couple of questions. % Run these commands in matlab % annotnames = strvcat('superiortemporal','insula','postcentral'); % annotvals = [1.1 2.2 3.7]; % annotfile = '~/paul_analysis/fsaverage/label/lh.aparc.annot'; % surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile); % clear mri % mri.vol = surfoverlay; % MRIwrite(mri,'vals.mgh'); %
- Correct me if I am wrong, the annotation values (annotvals) are
from results after correcting for multiple comparisons using mri_fdr?
They can be anything that you have one value per annotation.
- Is this correct way to add octave path to freesurfer's path?
Sorry, I have no idea
setenv FS_USE_OCTAVE 4.0.3
setenv FS_OCTAVE_LIB /Applications/octave/lib setenv FS_OCTAVE_BIN /Application/octave/binary Thanks, Best, Paul
On Thu, Apr 20, 2017 at 10:55 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
you can get it here https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
<https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m>
On 04/20/2017 10:10 AM, miracle ozzoude wrote: > Hello Doug, > I downloaded and installed octave. However, I can't find the > annotval2surfoverlay.m file in the matlab directory of freesurfer. > Does it come with FS v6 or do i need to download the file? Also, I was > looking into the annotval2surfoverlay file and I have couple of > questions. > % Run these commands in matlab > % annotnames = strvcat('superiortemporal','insula','postcentral'); > % annotvals = [1.1 2.2 3.7]; > % annotfile = '~/subjects/fsaverage/label/lh.aparc.annot'; > % surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile); > % clear mri > % mri.vol = surfoverlay; > % MRIwrite(mri,'vals.mgh'); > % > 1) Are the annotation values (annotvals) from results after correcting > for multiple comparisons using mri_fdr? > 2) Do I need to add octave path to freesurfer PATH like the example > below? > setenv FS_USE_OCTAVE 4.0.3 > > setenv FS_OCTAVE_LIB /Applications/octave/lib > setenv FS_OCTAVE_BIN /Application/octave/binary > > On Wed, Apr 19, 2017 at 3:39 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > I think that will work > > > On 04/19/2017 03:33 PM, miracle ozzoude wrote: > > Hello Doug, > > Do you think writing the script with octave can substitutefor
> matlab? > > I am using FS v6.0 and I have the annotval2surfoverlay.m. Thanks > > Best, > > Paul > > > > On Wed, Apr 19, 2017 at 1:47 PM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > Sorry, I don't have another solution for you. > > > > > > On 04/19/2017 01:42 PM, miracle ozzoude wrote: > > > Thanks Doug. However, I am running freesurfer analysis on my > > personal > > > computer and I don't have matlab. Also, I don't knowhow
> this matlab > > > script works/ matlab works. Any instructions on how to use > it or > > > alternate? Please and thank you. > > > Best, > > > Paul. > > > > > > On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve > > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > > > It is a table of data, so you can't visualize it > directly on > > anything. > > > You can try using annotval2surfoverlay.m to createa
> surface > > > overlay of > > > the data. > > > > > > > > > On 04/19/2017 10:05 AM, miracle ozzoude wrote: > > > > Hello Doug, > > > > It worked. The issue was due to formatting error > with the > > aparc > > > file. > > > > Also, I was trying to visualize the result on the > surface > > using > > > > freeview -f fsaverage/lh.pial -viewport 3d (clicking > > overlay on > > > > freeview and loading the sig.mgh). However, i got an > error " > > > failed to > > > > display overlay". How can I visualize the result? Thanks > > > > Best, > > > > Paul > > > > > > > > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve > > > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>> wrote: > > > > > > > > You have a table of data, so no template is > needed. If you > > > put the > > > > --surf before the --table, it probably runs, but it > > will ignore > > > > the surface > > > > > > > > > > > > On 4/18/17 9:58 PM, miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>> > > > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>>wrote:
> > > >> Thanks doug. Does it mean when using the --table > > flag, you > > > can't > > > >> use the fsaverage template? I came across several > > post in the > > > >> forum that used "--surf fsaverage lh " and it > worked. > > > >> Best, > > > >> Paul > > > >> > > > >> Sent from my BlackBerry 10 smartphone. > > > >> *From: *Douglas Greve > > > >> *Sent: *Tuesday, April 18, 2017 9:52 PM > > > >> *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > >> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > > > >> *Reply To: *Freesurfer support list > > > >> *Subject: *Re: [Freesurfer] mri_glmfit error > with aparc > > > table flag > > > >> > > > >> > > > >> Don't include --surf fsaverage lh. It thinks the > > input is a > > > >> surface, not a table > > > >> > > > >> > > > >> > > > >> On 4/18/17 9:21 PM, miracle ozzoude wrote: > > > >>> Hello freesurfer, > > > >>> I am trying to run mri_glmfit with the --table > flag. My > > > >>> aparc_lh_thick_stats.txt contain entorhinal and > > > parahippocampal > > > >>> thickness values for 32 subjects. I ran the glm > > command and > > > >>> received an error. Please, how can i solve this > > issue? I have > > > >>> included my command, fsgd file, contrast > matrix and > > error > > > below. > > > >>> Thanks > > > >>> Best, > > > >>> Paul > > > >>> > > > >>> GLM command: mri_glmfit --table > aparc_lh_thick_stats.txt > > > --fsgd > > > >>> age.fsgd --C age1.mtx --C age2.mtx --surf > fsaverage lh > > > --cortex > > > >>> --glmdir lh.thickness.glmdir > > > >>> > > > >>> > > > >>> ERROR= "gdfRead(): reading age.fsgd > > > >>> > > > >>> INFO: DeMeanFlag keyword not found, DeMeaning will > > NOT be > > > done. > > > >>> > > > >>> Continuous Variable Means (all subjects) > > > >>> > > > >>> 0 Age 39.9375 17.3312 > > > >>> > > > >>> Class Means of each Continuous Variable > > > >>> > > > >>> 1 Group1 35.6316 > > > >>> > > > >>> 2 Group2 46.2308 > > > >>> > > > >>> INFO: gd2mtx_method is dods > > > >>> > > > >>> Reading source surface > > > >>> > > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white
> > > >>> > > > >>> Number of vertices 163842 > > > >>> > > > >>> Number of faces 327680 > > > >>> > > > >>> Total area 65416.984375 > > > >>> > > > >>> AvgVtxArea 0.399269 > > > >>> > > > >>> AvgVtxDist 0.721953 > > > >>> > > > >>> StdVtxDist 0.195470 > > > >>> > > > >>> > > > >>> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 > > zkaufman > > > Exp $ > > > >>> > > > >>> cwd > /Users/MiracleOz/Documents/improvervsdeclinermri > > > >>> > > > >>> cmdline mri_glmfit.bin --table > > aparc_lh_thick_stats.txt --fsgd > > > >>> age.fsgd --C age1.mtx --C age2.mtx --surf > fsaverage lh > > > --cortex > > > >>> --glmdir lh.thickness.glmdir > > > >>> > > > >>> sysname Darwin > > > >>> > > > >>> hostname MacBook-Pro.local > > > >>> > > > >>> machine x86_64 > > > >>> > > > >>> user MiracleOz > > > >>> > > > >>> FixVertexAreaFlag = 1 > > > >>> > > > >>> UseMaskWithSmoothing 1 > > > >>> > > > >>> OneSampleGroupMean 0 > > > >>> > > > >>> y > > > >>> > > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
> > > >>> > > > >>> logyflag 0 > > > >>> > > > >>> usedti 0 > > > >>> > > > >>> FSGD age.fsgd > > > >>> > > > >>> labelmask > > > >>> > > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label
> > > >>> > > > >>> maskinv 0 > > > >>> > > > >>> glmdir lh.thickness.glmdir > > > >>> > > > >>> IllCondOK 0 > > > >>> > > > >>> ReScaleX 1 > > > >>> > > > >>> DoFFx 0 > > > >>> > > > >>> Creating output directory lh.thickness.glmdir > > > >>> > > > >>> Loading y from > > > >>> > > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
> > > >>> > > > >>> Found 66 data colums > > > >>> > > > >>> Found 0 data rows > > > >>> > > > >>> INFO: gd2mtx_method is dods > > > >>> > > > >>> Saving design matrix to lh.thickness.glmdir/Xg.dat > > > >>> > > > >>> Computing normalized matrix > > > >>> > > > >>> Normalized matrix condition is 32.2165 > > > >>> > > > >>> Matrix condition is 20734.7 > > > >>> > > > >>> Found 149955 points in label. > > > >>> > > > >>> ERROR: mri_reshape: number of elements cannot > change > > > >>> > > > >>> nv1 = 163842, nv1 = 66 > > > >>> > > > >>> search space = 82219.962936 > > > >>> > > > >>> ERROR: dimension mismatch between y and X. > > > >>> > > > >>> y has 0 inputs, X has 32 rows." > > > >>> > > > >>> FSGD file: GroupDescriptorFile 1 > > > >>> > > > >>> Title MOT > > > >>> > > > >>> Class Group1 > > > >>> > > > >>> Class Group2 > > > >>> > > > >>> Variables Age > > > >>> > > > >>> Input 01053p Group1 23 > > > >>> > > > >>> Input 01054p Group1 43 > > > >>> > > > >>> Input 01061p Group2 39 > > > >>> > > > >>> Input 01062p Group2 19 > > > >>> > > > >>> Input 01074p Group2 28 > > > >>> > > > >>> .............. (I have more participants) > > > >>> > > > >>> > > > >>> CONTRAST MATRIX: 1 -1 0 0 > > > >>> > > > >>> > > > >>> > > > >>> ______________________________
> > > >>> Freesurfer mailing list > > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu 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<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >> > > 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<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > >> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>>> > > > > _______________________________________________ > Freesurfer > > > mailing > > > > list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>>>The
> > > > information in this e-mail is intended only for > the person > > > to whom > > > > it is addressed. If you believe this e-mail was sent > > to you in > > > > error and the e-mail contains patient > information, please > > > contact > > > > the Partners Compliance HelpLine at > > > > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> > > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>>> > > > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> > > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>>>> . If the e-mail wassent
> > > > to you in error but does not contain patient > > information, please > > > > contact the sender and properly dispose ofthe
> e-mail. > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
<tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>> > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>>> > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>> > > > Outgoing: > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>>> > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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participants (4)
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Douglas Greve -
Douglas N Greve
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miracle ozzoude -
miracooloz＠gmail.com