Hello Experts,
I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page ( https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you.
Best, Paul
*Script*: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx
#resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
# #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh
# #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir
# # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
*Fsgd file 1:pairs.fsgd*
GroupDescriptorFile 1
Class ADEX
Input 1000_1 ADEX
Input 1000_2 ADEX
Input 1001_1 ADEX
Input 1001_2 ADEX
Input 1003_1 ADEX
Input 1003_2 ADEX
Input 1005_1 ADEX
Input 1005_2 ADEX
Input 1008_1 ADEX
Input 1008_2 ADEX
Input 1013_1 ADEX
Input 1013_2 ADEX
Input 1014_1 ADEX
Input 1014_2 ADEX
*Fsgd file 2: paired_diff.fsgd*
GroupDescriptorFile 1
Class ADEX
Variables Age
Input 1000 ADEX 72
Input 1001 ADEX 76
Input 1003 ADEX 72
Input 1005 ADEX 80
Input 1008 ADEX 72
Input 1013 ADEX 80
Input 1014 ADEX 80
Why are you doing your own MC simulation? You can just use the tables that we distribute ...
On 1/17/18 6:12 PM, miracle ozzoude wrote:
Hello Experts,
I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you.
Best, Paul
*Script*: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx #resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh # #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite *Fsgd file 1:pairs.fsgd*
GroupDescriptorFile 1
Class ADEX
Input 1000_1 ADEX
Input 1000_2 ADEX
Input 1001_1 ADEX
Input 1001_2 ADEX
Input 1003_1 ADEX
Input 1003_2 ADEX
Input 1005_1 ADEX
Input 1005_2 ADEX
Input 1008_1 ADEX
Input 1008_2 ADEX
Input 1013_1 ADEX
Input 1013_2 ADEX
Input 1014_1 ADEX
Input 1014_2 ADEX
*Fsgd file 2: paired_diff.fsgd*
GroupDescriptorFile 1
Class ADEX
Variables Age
Input 1000 ADEX 72
Input 1001 ADEX 76
Input 1003 ADEX 72
Input 1005 ADEX 80
Input 1008 ADEX 72
Input 1013 ADEX 80
Input 1014 ADEX 80
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Doug, Thanks for responding. I am running a whole brain analysis as result shouldn’t I build my own MC simulation? Best, Paul
Sent from my iPhone
On Jan 18, 2018, at 5:23 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Why are you doing your own MC simulation? You can just use the tables that we distribute ...
On 1/17/18 6:12 PM, miracle ozzoude wrote: Hello Experts,
I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you.
Best, Paul
Script: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx
#resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
# #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh
# #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir
# # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
Fsgd file 1:pairs.fsgd GroupDescriptorFile 1
Class ADEX
Input 1000_1 ADEX
Input 1000_2 ADEX
Input 1001_1 ADEX
Input 1001_2 ADEX
Input 1003_1 ADEX
Input 1003_2 ADEX
Input 1005_1 ADEX
Input 1005_2 ADEX
Input 1008_1 ADEX
Input 1008_2 ADEX
Input 1013_1 ADEX
Input 1013_2 ADEX
Input 1014_1 ADEX
Input 1014_2 ADEX
Fsgd file 2: paired_diff.fsgd
GroupDescriptorFile 1
Class ADEX
Variables Age
Input 1000 ADEX 72
Input 1001 ADEX 76
Input 1003 ADEX 72
Input 1005 ADEX 80
Input 1008 ADEX 72
Input 1013 ADEX 80
Input 1014 ADEX 80
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
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.
Hello Doug,
I tried using the MC tables that FS distributed. However, i got an error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3 on mac. Thank you.
Best, Paul
mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite
On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Why are you doing your own MC simulation? You can just use the tables that we distribute ...
On 1/17/18 6:12 PM, miracle ozzoude wrote:
Hello Experts,
I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page (https://surfer.nmr.mgh.harvard.edu/fswiki/ PairedAnalysis). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you.
Best, Paul
*Script*: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx #resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh # #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite *Fsgd file 1:pairs.fsgd*
GroupDescriptorFile 1
Class ADEX
Input 1000_1 ADEX
Input 1000_2 ADEX
Input 1001_1 ADEX
Input 1001_2 ADEX
Input 1003_1 ADEX
Input 1003_2 ADEX
Input 1005_1 ADEX
Input 1005_2 ADEX
Input 1008_1 ADEX
Input 1008_2 ADEX
Input 1013_1 ADEX
Input 1013_2 ADEX
Input 1014_1 ADEX
Input 1014_2 ADEX *Fsgd file 2: paired_diff.fsgd*
GroupDescriptorFile 1
Class ADEX
Variables Age
Input 1000 ADEX 72
Input 1001 ADEX 76
Input 1003 ADEX 72
Input 1005 ADEX 80
Input 1008 ADEX 72
Input 1013 ADEX 80
Input 1014 ADEX 80
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.
---------- Forwarded message ---------- From: miracle ozzoude miracooloz@gmail.com Date: Sat, Jan 20, 2018 at 1:56 PM Subject: Re: [Freesurfer] monte-carlo error in longitudinal pipeline To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hello Doug,
I tried using the MC tables that FS distributed. However, i got an error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3 on mac. Thank you.
Best, Paul
mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite
On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Why are you doing your own MC simulation? You can just use the tables that we distribute ...
On 1/17/18 6:12 PM, miracle ozzoude wrote:
Hello Experts,
I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page (https://surfer.nmr.mgh.harvar d.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you.
Best, Paul
*Script*: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx #resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh # #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite *Fsgd file 1:pairs.fsgd*
GroupDescriptorFile 1
Class ADEX
Input 1000_1 ADEX
Input 1000_2 ADEX
Input 1001_1 ADEX
Input 1001_2 ADEX
Input 1003_1 ADEX
Input 1003_2 ADEX
Input 1005_1 ADEX
Input 1005_2 ADEX
Input 1008_1 ADEX
Input 1008_2 ADEX
Input 1013_1 ADEX
Input 1013_2 ADEX
Input 1014_1 ADEX
Input 1014_2 ADEX *Fsgd file 2: paired_diff.fsgd*
GroupDescriptorFile 1
Class ADEX
Variables Age
Input 1000 ADEX 72
Input 1001 ADEX 76
Input 1003 ADEX 72
Input 1005 ADEX 80
Input 1008 ADEX 72
Input 1013 ADEX 80
Input 1014 ADEX 80
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.
If your fwhm is 0, then something is wrong. Look in the fwhm.dat file in the glmfit output to see what the value is. Also, send the terminal output from mri_glmfit (not mri_glmfit-sim)
On 01/22/2018 11:43 AM, miracle ozzoude wrote:
---------- Forwarded message ---------- From: *miracle ozzoude* <miracooloz@gmail.com mailto:miracooloz@gmail.com> Date: Sat, Jan 20, 2018 at 1:56 PM Subject: Re: [Freesurfer] monte-carlo error in longitudinal pipeline To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
Hello Doug,
I tried using the MC tables that FS distributed. However, i got an error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3 on mac. Thank you.
Best, Paul
mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite
On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Why are you doing your own MC simulation? You can just use the tables that we distribute ... On 1/17/18 6:12 PM, miracle ozzoude wrote:Hello Experts, I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you. Best, Paul *Script*: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx #resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh # #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite *Fsgd file 1:pairs.fsgd* GroupDescriptorFile 1 Class ADEX Input 1000_1 ADEX Input 1000_2 ADEX Input 1001_1 ADEX Input 1001_2 ADEX Input 1003_1 ADEX Input 1003_2 ADEX Input 1005_1 ADEX Input 1005_2 ADEX Input 1008_1 ADEX Input 1008_2 ADEX Input 1013_1 ADEX Input 1013_2 ADEX Input 1014_1 ADEX Input 1014_2 ADEX *Fsgd file 2: paired_diff.fsgd* GroupDescriptorFile 1 Class ADEX Variables Age Input 1000 ADEX 72 Input 1001 ADEX 76 Input 1003 ADEX 72 Input 1005 ADEX 80 Input 1008 ADEX 72 Input 1013 ADEX 80 Input 1014 ADEX 80 _______________________________________________ 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
Hello Doug,
I looked at the fwhm.dat and fwhm value = 0. I have attached the mri_glmfit.log file. How do i solve this problem?
Best, Paul
On Mon, Jan 22, 2018 at 11:57 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
If your fwhm is 0, then something is wrong. Look in the fwhm.dat file in the glmfit output to see what the value is. Also, send the terminal output from mri_glmfit (not mri_glmfit-sim)
On 01/22/2018 11:43 AM, miracle ozzoude wrote:
---------- Forwarded message ---------- From: *miracle ozzoude* <miracooloz@gmail.com mailto:miracooloz@gmail.com> Date: Sat, Jan 20, 2018 at 1:56 PM Subject: Re: [Freesurfer] monte-carlo error in longitudinal pipeline To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
Hello Doug,
I tried using the MC tables that FS distributed. However, i got an error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3 on mac. Thank you.
Best, Paul
mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite
On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Why are you doing your own MC simulation? You can just use the tables that we distribute ... On 1/17/18 6:12 PM, miracle ozzoude wrote:Hello Experts, I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you. Best, Paul *Script*: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx #resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh # #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite *Fsgd file 1:pairs.fsgd* GroupDescriptorFile 1 Class ADEX Input 1000_1 ADEX Input 1000_2 ADEX Input 1001_1 ADEX Input 1001_2 ADEX Input 1003_1 ADEX Input 1003_2 ADEX Input 1005_1 ADEX Input 1005_2 ADEX Input 1008_1 ADEX Input 1008_2 ADEX Input 1013_1 ADEX Input 1013_2 ADEX Input 1014_1 ADEX Input 1014_2 ADEX *Fsgd file 2: paired_diff.fsgd* GroupDescriptorFile 1 Class ADEX Variables Age Input 1000 ADEX 72 Input 1001 ADEX 76 Input 1003 ADEX 72 Input 1005 ADEX 80 Input 1008 ADEX 72 Input 1013 ADEX 80 Input 1014 ADEX 80 _______________________________________________ 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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-- 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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can you send the terminal output of mri_glmfit?
On 01/24/2018 02:52 PM, miracle ozzoude wrote:
Hello Doug,
I looked at the fwhm.dat and fwhm value = 0. I have attached the mri_glmfit.log file. How do i solve this problem?
Best, Paul
On Mon, Jan 22, 2018 at 11:57 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If your fwhm is 0, then something is wrong. Look in the fwhm.dat file in the glmfit output to see what the value is. Also, send the terminal output from mri_glmfit (not mri_glmfit-sim) On 01/22/2018 11:43 AM, miracle ozzoude wrote: > > ---------- Forwarded message ---------- > From: *miracle ozzoude* <miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > Date: Sat, Jan 20, 2018 at 1:56 PM > Subject: Re: [Freesurfer] monte-carlo error in longitudinal pipeline > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > Hello Doug, > > I tried using the MC tables that FS distributed. However, i got an > error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and > there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are > my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is > stable version 5.3 on mac. Thank you. > > Best, > Paul > > mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos > --cwpvalthresh 0.05 --2spaces --overwrite > mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos > --cwpvalthresh 0.05 --2spaces --overwrite > > On Thu, Jan 18, 2018 at 5:23 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: > > Why are you doing your own MC simulation? You can just use the > tables that we distribute ... > > > On 1/17/18 6:12 PM, miracle ozzoude wrote: >> Hello Experts, >> >> I am running a paired t-test cortical thickness analysis based on >> the instruction on the wiki page >> (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis> >> <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>>). >> However, the monte carlo files weren't not created when i >> corrected for multiple comparisons. Below are my script, fsgd >> files, mc-z log file, and a screenshot of contrast folder missing >> mc.z maps. Please can you help me figure out why the error is >> happening. Thank you. >> >> Best, >> Paul >> >> *Script*: >> pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx >> martrix2=age.mtx >> #resample each subjects's left and right hemisphere data to >> fsavarage. >> mris_preproc --target fsaverage --hemi lh --meas thickness --out >> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff >> mris_preproc --target fsaverage --hemi rh --meas thickness --out >> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff >> # #smoothen the concatenated file by 5mm FWHM. --cortex means >> only smooth areas in the cortex. N:B. FWHM changes based on study >> type. >> mri_surf2surf --hemi lh --s fsaverage --sval >> lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval >> lh.paired-diff.thickness.sm05.mgh >> mri_surf2surf --hemi rh --s fsaverage --sval >> rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval >> rh.paired-diff.thickness.sm05.mgh >> # #Run GLM analysis >> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired >> --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir >> lh.paired-diff.glmdirir >> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired >> --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir >> rh.paired-diff.glmdir >> # # #Run Clusterwise correction for multiple comparisons using >> MONTE CARLO. First create a table for of simulations >> mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 >> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite >> mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 >> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite >> *Fsgd file 1:pairs.fsgd* >> >> GroupDescriptorFile 1 >> >> Class ADEX >> >> Input 1000_1 ADEX >> >> Input 1000_2 ADEX >> >> Input 1001_1 ADEX >> >> Input 1001_2 ADEX >> >> Input 1003_1 ADEX >> >> Input 1003_2 ADEX >> >> Input 1005_1 ADEX >> >> Input 1005_2 ADEX >> >> Input 1008_1 ADEX >> >> Input 1008_2 ADEX >> >> Input 1013_1 ADEX >> >> Input 1013_2 ADEX >> >> Input 1014_1 ADEX >> >> Input 1014_2 ADEX >> >> *Fsgd file 2: paired_diff.fsgd* >> >> GroupDescriptorFile 1 >> >> Class ADEX >> >> Variables Age >> >> Input 1000 ADEX 72 >> >> Input 1001 ADEX 76 >> >> Input 1003 ADEX 72 >> >> Input 1005 ADEX 80 >> >> Input 1008 ADEX 72 >> >> Input 1013 ADEX 80 >> >> Input 1014 ADEX 80 >> >> >> >> _______________________________________________ >> 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
Hello Doug,
Thanks for the patience. Here's the output from the terminal when I ran mri_glmfit.
Best, Paul
/Applications/freesurfer
START: LONGITUDINAL CORTICAL THICKNESS
1000
1000_1
1000_1.long.1000
1000_2
1000_2.long.1000
1001
1001_1
1001_1.long.1001
1001_2
1001_2.long.1001
1003
1003_1
1003_1.long.1003
1003_2
1003_2.long.1003
1005
1005_1
1005_1.long.1005
1005_2
1005_2.long.1005
1008
1008_1
1008_1.long.1008
1008_2
1008_2.long.1008
1013
1013_1
1013_1.long.1013
1013_2
1013_2.long.1013
1014
1014_1
1014_1.long.1014
1014_2
1014_2.long.1014
gdfReadHeader: reading paired_diff.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 76 3.70328
Class Means of each Continuous Variable
1 ADEX 76.0000
INFO: gd2mtx_method is doss
Reading source surface /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.648438
AvgVtxArea 0.399267
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018
cmdline mri_glmfit --y lh.paired.diff.thickness.10.mgh --fsgd paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage lh --cortex --glmdir lh.paired.diff.glmdir
sysname Darwin
hostname opennet-33-172.uhnres.utoronto.ca
machine x86_64
user carm
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh
logyflag 0
usedti 0
FSGD paired_diff.fsgd
labelmask /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.paired.diff.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.paired.diff.glmdir
Loading y from /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh
INFO: gd2mtx_method is doss
Saving design matrix to lh.paired.diff.glmdir/Xg.dat
Normalized matrix condition is 1686.7
Matrix condition is 2.46289e+06
Found 149955 points in label.
Pruning voxels by thr: 0.000000
Found 0 voxels in mask
Saving mask to lh.paired.diff.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 0.000000
DOF = 5
Starting fit and test
Fit completed in 8.33333e-05 minutes
Computing spatial AR1 on surface
WARNING: ar1 = nan <= 0. Setting fwhm to 0.
Residual: ar1mn=nan, ar1std=nan, gstd=0.000000, fwhm=0.000000
Writing results
mean
maxvox sig=0 F=0 at index 0 0 0 seed=1517221145
age
maxvox sig=0 F=0 at index 0 0 0 seed=1517221145
mri_glmfit done
gdfReadHeader: reading paired_diff.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 76 3.70328
Class Means of each Continuous Variable
1 ADEX 76.0000
INFO: gd2mtx_method is doss
Reading source surface /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/surf/rh.white
Number of vertices 163842
Number of faces 327680
Total area 65020.765625
AvgVtxArea 0.396850
AvgVtxDist 0.717994
StdVtxDist 0.193566
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018
cmdline mri_glmfit --y rh.paired.diff.thickness.10.mgh --fsgd paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage rh --cortex --glmdir rh.paired.diff.glmdir
sysname Darwin
hostname opennet-33-172.uhnres.utoronto.ca
machine x86_64
user carm
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh
logyflag 0
usedti 0
FSGD paired_diff.fsgd
labelmask /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/label/rh.cortex.label
maskinv 0
glmdir rh.paired.diff.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory rh.paired.diff.glmdir
Loading y from /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh
INFO: gd2mtx_method is doss
Saving design matrix to rh.paired.diff.glmdir/Xg.dat
Normalized matrix condition is 1686.7
Matrix condition is 2.46289e+06
Found 149926 points in label.
Pruning voxels by thr: 0.000000
Found 0 voxels in mask
Saving mask to rh.paired.diff.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 0.000000
DOF = 5
Starting fit and test
Fit completed in 0.0001 minutes
Computing spatial AR1 on surface
WARNING: ar1 = nan <= 0. Setting fwhm to 0.
Residual: ar1mn=nan, ar1std=nan, gstd=0.000000, fwhm=0.000000
Writing results
mean
maxvox sig=0 F=0 at index 0 0 0 seed=1517884366
age
maxvox sig=0 F=0 at index 0 0 0 seed=1517884366
mri_glmfit done
On Wed, Jan 24, 2018 at 2:59 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you send the terminal output of mri_glmfit?
On 01/24/2018 02:52 PM, miracle ozzoude wrote:
Hello Doug,
I looked at the fwhm.dat and fwhm value = 0. I have attached the mri_glmfit.log file. How do i solve this problem?
Best, Paul
On Mon, Jan 22, 2018 at 11:57 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If your fwhm is 0, then something is wrong. Look in the fwhm.dat file in the glmfit output to see what the value is. Also, send the terminal output from mri_glmfit (not mri_glmfit-sim) On 01/22/2018 11:43 AM, miracle ozzoude wrote: > > ---------- Forwarded message ---------- > From: *miracle ozzoude* <miracooloz@gmail.com <mailto:miracooloz@gmail.com>
> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > Date: Sat, Jan 20, 2018 at 1:56 PM > Subject: Re: [Freesurfer] monte-carlo error in longitudinalpipeline
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > Hello Doug, > > I tried using the MC tables that FS distributed. However, i got an > error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checkedand
> there's no fwhm00, the table starts from fwhm01 to fwhm30. Beloware
> my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is > stable version 5.3 on mac. Thank you. > > Best, > Paul > > mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos > --cwpvalthresh 0.05 --2spaces --overwrite > mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos > --cwpvalthresh 0.05 --2spaces --overwrite > > On Thu, Jan 18, 2018 at 5:23 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: > > Why are you doing your own MC simulation? You can just use the > tables that we distribute ... > > > On 1/17/18 6:12 PM, miracle ozzoude wrote: >> Hello Experts, >> >> I am running a paired t-test cortical thickness analysis based on >> the instruction on the wiki page >> (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis> >> <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>>). >> However, the monte carlo files weren't not created when i >> corrected for multiple comparisons. Below are my script, fsgd >> files, mc-z log file, and a screenshot of contrast folder missing >> mc.z maps. Please can you help me figure out why the error is >> happening. Thank you. >> >> Best, >> Paul >> >> *Script*: >> pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx >> martrix2=age.mtx >> #resample each subjects's left and right hemisphere data to >> fsavarage. >> mris_preproc --target fsaverage --hemi lh --meas thickness --out >> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff >> mris_preproc --target fsaverage --hemi rh --meas thickness --out >> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff >> # #smoothen the concatenated file by 5mm FWHM. --cortex means >> only smooth areas in the cortex. N:B. FWHM changes based on study >> type. >> mri_surf2surf --hemi lh --s fsaverage --sval >> lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval >> lh.paired-diff.thickness.sm05.mgh >> mri_surf2surf --hemi rh --s fsaverage --sval >> rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval >> rh.paired-diff.thickness.sm05.mgh >> # #Run GLM analysis >> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd$paired
>> --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir >> lh.paired-diff.glmdirir >> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd$paired
>> --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir >> rh.paired-diff.glmdir >> # # #Run Clusterwise correction for multiple comparisons using >> MONTE CARLO. First create a table for of simulations >> mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 >> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite >> mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 >> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite >> *Fsgd file 1:pairs.fsgd* >> >> GroupDescriptorFile 1 >> >> Class ADEX >> >> Input 1000_1 ADEX >> >> Input 1000_2 ADEX >> >> Input 1001_1 ADEX >> >> Input 1001_2 ADEX >> >> Input 1003_1 ADEX >> >> Input 1003_2 ADEX >> >> Input 1005_1 ADEX >> >> Input 1005_2 ADEX >> >> Input 1008_1 ADEX >> >> Input 1008_2 ADEX >> >> Input 1013_1 ADEX >> >> Input 1013_2 ADEX >> >> Input 1014_1 ADEX >> >> Input 1014_2 ADEX >> >> *Fsgd file 2: paired_diff.fsgd* >> >> GroupDescriptorFile 1 >> >> Class ADEX >> >> Variables Age >> >> Input 1000 ADEX 72 >> >> Input 1001 ADEX 76 >> >> Input 1003 ADEX 72 >> >> Input 1005 ADEX 80 >> >> Input 1008 ADEX 72 >> >> Input 1013 ADEX 80 >> >> Input 1014 ADEX 80 >> >> >> >> _______________________________________________ >> 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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---------- Forwarded message ---------- From: miracle ozzoude miracooloz@gmail.com Date: Fri, Jan 26, 2018 at 7:08 PM Subject: Re: [Freesurfer] Fwd: monte-carlo error in longitudinal pipeline To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hello Doug,
Thanks for the patience. Here's the output from the terminal when I ran mri_glmfit.
Best, Paul
/Applications/freesurfer
START: LONGITUDINAL CORTICAL THICKNESS
1000
1000_1
1000_1.long.1000
1000_2
1000_2.long.1000
1001
1001_1
1001_1.long.1001
1001_2
1001_2.long.1001
1003
1003_1
1003_1.long.1003
1003_2
1003_2.long.1003
1005
1005_1
1005_1.long.1005
1005_2
1005_2.long.1005
1008
1008_1
1008_1.long.1008
1008_2
1008_2.long.1008
1013
1013_1
1013_1.long.1013
1013_2
1013_2.long.1013
1014
1014_1
1014_1.long.1014
1014_2
1014_2.long.1014
gdfReadHeader: reading paired_diff.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 76 3.70328
Class Means of each Continuous Variable
1 ADEX 76.0000
INFO: gd2mtx_method is doss
Reading source surface /Users/carm/Documents/Cas/ ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.648438
AvgVtxArea 0.399267
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018
cmdline mri_glmfit --y lh.paired.diff.thickness.10.mgh --fsgd paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage lh --cortex --glmdir lh.paired.diff.glmdir
sysname Darwin
hostname opennet-33-172.uhnres.utoronto.ca
machine x86_64
user carm
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_ Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh
logyflag 0
usedti 0
FSGD paired_diff.fsgd
labelmask /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_ Analysis_Jan9_2018/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.paired.diff.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.paired.diff.glmdir
Loading y from /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_ Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh
INFO: gd2mtx_method is doss
Saving design matrix to lh.paired.diff.glmdir/Xg.dat
Normalized matrix condition is 1686.7
Matrix condition is 2.46289e+06
Found 149955 points in label.
Pruning voxels by thr: 0.000000
Found 0 voxels in mask
Saving mask to lh.paired.diff.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 0.000000
DOF = 5
Starting fit and test
Fit completed in 8.33333e-05 minutes
Computing spatial AR1 on surface
WARNING: ar1 = nan <= 0. Setting fwhm to 0.
Residual: ar1mn=nan, ar1std=nan, gstd=0.000000, fwhm=0.000000
Writing results
mean
maxvox sig=0 F=0 at index 0 0 0 seed=1517221145
age
maxvox sig=0 F=0 at index 0 0 0 seed=1517221145
mri_glmfit done
gdfReadHeader: reading paired_diff.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 76 3.70328
Class Means of each Continuous Variable
1 ADEX 76.0000
INFO: gd2mtx_method is doss
Reading source surface /Users/carm/Documents/Cas/ ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/surf/rh.white
Number of vertices 163842
Number of faces 327680
Total area 65020.765625
AvgVtxArea 0.396850
AvgVtxDist 0.717994
StdVtxDist 0.193566
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018
cmdline mri_glmfit --y rh.paired.diff.thickness.10.mgh --fsgd paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage rh --cortex --glmdir rh.paired.diff.glmdir
sysname Darwin
hostname opennet-33-172.uhnres.utoronto.ca
machine x86_64
user carm
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_ Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh
logyflag 0
usedti 0
FSGD paired_diff.fsgd
labelmask /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_ Analysis_Jan9_2018/fsaverage/label/rh.cortex.label
maskinv 0
glmdir rh.paired.diff.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory rh.paired.diff.glmdir
Loading y from /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_ Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh
INFO: gd2mtx_method is doss
Saving design matrix to rh.paired.diff.glmdir/Xg.dat
Normalized matrix condition is 1686.7
Matrix condition is 2.46289e+06
Found 149926 points in label.
Pruning voxels by thr: 0.000000
Found 0 voxels in mask
Saving mask to rh.paired.diff.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 0.000000
DOF = 5
Starting fit and test
Fit completed in 0.0001 minutes
Computing spatial AR1 on surface
WARNING: ar1 = nan <= 0. Setting fwhm to 0.
Residual: ar1mn=nan, ar1std=nan, gstd=0.000000, fwhm=0.000000
Writing results
mean
maxvox sig=0 F=0 at index 0 0 0 seed=1517884366
age
maxvox sig=0 F=0 at index 0 0 0 seed=1517884366
mri_glmfit done
On Wed, Jan 24, 2018 at 2:59 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you send the terminal output of mri_glmfit?
On 01/24/2018 02:52 PM, miracle ozzoude wrote:
Hello Doug,
I looked at the fwhm.dat and fwhm value = 0. I have attached the mri_glmfit.log file. How do i solve this problem?
Best, Paul
On Mon, Jan 22, 2018 at 11:57 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If your fwhm is 0, then something is wrong. Look in the fwhm.dat file in the glmfit output to see what the value is. Also, send the terminal output from mri_glmfit (not mri_glmfit-sim) On 01/22/2018 11:43 AM, miracle ozzoude wrote: > > ---------- Forwarded message ---------- > From: *miracle ozzoude* <miracooloz@gmail.com <mailto:miracooloz@gmail.com>
> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > Date: Sat, Jan 20, 2018 at 1:56 PM > Subject: Re: [Freesurfer] monte-carlo error in longitudinalpipeline
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > Hello Doug, > > I tried using the MC tables that FS distributed. However, i got an > error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checkedand
> there's no fwhm00, the table starts from fwhm01 to fwhm30. Beloware
> my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is > stable version 5.3 on mac. Thank you. > > Best, > Paul > > mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos > --cwpvalthresh 0.05 --2spaces --overwrite > mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos > --cwpvalthresh 0.05 --2spaces --overwrite > > On Thu, Jan 18, 2018 at 5:23 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: > > Why are you doing your own MC simulation? You can just use the > tables that we distribute ... > > > On 1/17/18 6:12 PM, miracle ozzoude wrote: >> Hello Experts, >> >> I am running a paired t-test cortical thickness analysis based on >> the instruction on the wiki page >> (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis> >> <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>>). >> However, the monte carlo files weren't not created when i >> corrected for multiple comparisons. Below are my script, fsgd >> files, mc-z log file, and a screenshot of contrast folder missing >> mc.z maps. Please can you help me figure out why the error is >> happening. Thank you. >> >> Best, >> Paul >> >> *Script*: >> pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx >> martrix2=age.mtx >> #resample each subjects's left and right hemisphere data to >> fsavarage. >> mris_preproc --target fsaverage --hemi lh --meas thickness --out >> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff >> mris_preproc --target fsaverage --hemi rh --meas thickness --out >> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff >> # #smoothen the concatenated file by 5mm FWHM. --cortex means >> only smooth areas in the cortex. N:B. FWHM changes based on study >> type. >> mri_surf2surf --hemi lh --s fsaverage --sval >> lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval >> lh.paired-diff.thickness.sm05.mgh >> mri_surf2surf --hemi rh --s fsaverage --sval >> rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval >> rh.paired-diff.thickness.sm05.mgh >> # #Run GLM analysis >> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd$paired
>> --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir >> lh.paired-diff.glmdirir >> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd$paired
>> --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir >> rh.paired-diff.glmdir >> # # #Run Clusterwise correction for multiple comparisons using >> MONTE CARLO. First create a table for of simulations >> mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 >> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite >> mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 >> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite >> *Fsgd file 1:pairs.fsgd* >> >> GroupDescriptorFile 1 >> >> Class ADEX >> >> Input 1000_1 ADEX >> >> Input 1000_2 ADEX >> >> Input 1001_1 ADEX >> >> Input 1001_2 ADEX >> >> Input 1003_1 ADEX >> >> Input 1003_2 ADEX >> >> Input 1005_1 ADEX >> >> Input 1005_2 ADEX >> >> Input 1008_1 ADEX >> >> Input 1008_2 ADEX >> >> Input 1013_1 ADEX >> >> Input 1013_2 ADEX >> >> Input 1014_1 ADEX >> >> Input 1014_2 ADEX >> >> *Fsgd file 2: paired_diff.fsgd* >> >> GroupDescriptorFile 1 >> >> Class ADEX >> >> Variables Age >> >> Input 1000 ADEX 72 >> >> Input 1001 ADEX 76 >> >> Input 1003 ADEX 72 >> >> Input 1005 ADEX 80 >> >> Input 1008 ADEX 72 >> >> Input 1013 ADEX 80 >> >> Input 1014 ADEX 80 >> >> >> >> _______________________________________________ >> 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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something is wrong with the mask (the terminal output says that there are no voxels in the mask)
On 1/30/18 11:51 AM, miracle ozzoude wrote:
---------- Forwarded message ---------- From: *miracle ozzoude* <miracooloz@gmail.com mailto:miracooloz@gmail.com> Date: Fri, Jan 26, 2018 at 7:08 PM Subject: Re: [Freesurfer] Fwd: monte-carlo error in longitudinal pipeline To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
Hello Doug,
Thanks for the patience. Here's the output from the terminal when I ran mri_glmfit.
Best, Paul
/Applications/freesurfer
START: LONGITUDINAL CORTICAL THICKNESS
1000
1000_1
1000_1.long.1000
1000_2
1000_2.long.1000
1001
1001_1
1001_1.long.1001
1001_2
1001_2.long.1001
1003
1003_1
1003_1.long.1003
1003_2
1003_2.long.1003
1005
1005_1
1005_1.long.1005
1005_2
1005_2.long.1005
1008
1008_1
1008_1.long.1008
1008_2
1008_2.long.1008
1013
1013_1
1013_1.long.1013
1013_2
1013_2.long.1013
1014
1014_1
1014_1.long.1014
1014_2
1014_2.long.1014
gdfReadHeader: reading paired_diff.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 76 3.70328
Class Means of each Continuous Variable
1 ADEX76.0000
INFO: gd2mtx_method is doss
Reading source surface /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65416.648438
AvgVtxArea 0.399267
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018
cmdline mri_glmfit --y lh.paired.diff.thickness.10.mgh --fsgd paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage lh --cortex --glmdir lh.paired.diff.glmdir
sysnameDarwin
hostname opennet-33-172.uhnres.utoronto.ca http://opennet-33-172.uhnres.utoronto.ca
machinex86_64
user carm
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh
logyflag 0
usedti0
FSGD paired_diff.fsgd
labelmask/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.paired.diff.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.paired.diff.glmdir
Loading y from /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh
INFO: gd2mtx_method is doss
Saving design matrix to lh.paired.diff.glmdir/Xg.dat
Normalized matrix condition is 1686.7
Matrix condition is 2.46289e+06
Found 149955 points in label.
Pruning voxels by thr: 0.000000
Found 0 voxels in mask
Saving mask to lh.paired.diff.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 0.000000
DOF = 5
Starting fit and test
Fit completed in 8.33333e-05 minutes
Computing spatial AR1 on surface
WARNING: ar1 = nan <= 0. Setting fwhm to 0.
Residual: ar1mn=nan, ar1std=nan, gstd=0.000000, fwhm=0.000000
Writing results
mean
maxvox sig=0F=0atindex 0 0 0seed=1517221145
age
maxvox sig=0F=0atindex 0 0 0seed=1517221145
mri_glmfit done
gdfReadHeader: reading paired_diff.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 76 3.70328
Class Means of each Continuous Variable
1 ADEX76.0000
INFO: gd2mtx_method is doss
Reading source surface /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/surf/rh.white
Number of vertices 163842
Number of faces327680
Total area 65020.765625
AvgVtxArea 0.396850
AvgVtxDist 0.717994
StdVtxDist 0.193566
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018
cmdline mri_glmfit --y rh.paired.diff.thickness.10.mgh --fsgd paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage rh --cortex --glmdir rh.paired.diff.glmdir
sysnameDarwin
hostname opennet-33-172.uhnres.utoronto.ca http://opennet-33-172.uhnres.utoronto.ca
machinex86_64
user carm
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh
logyflag 0
usedti0
FSGD paired_diff.fsgd
labelmask/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/label/rh.cortex.label
maskinv 0
glmdir rh.paired.diff.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory rh.paired.diff.glmdir
Loading y from /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh
INFO: gd2mtx_method is doss
Saving design matrix to rh.paired.diff.glmdir/Xg.dat
Normalized matrix condition is 1686.7
Matrix condition is 2.46289e+06
Found 149926 points in label.
Pruning voxels by thr: 0.000000
Found 0 voxels in mask
Saving mask to rh.paired.diff.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 0.000000
DOF = 5
Starting fit and test
Fit completed in 0.0001 minutes
Computing spatial AR1 on surface
WARNING: ar1 = nan <= 0. Setting fwhm to 0.
Residual: ar1mn=nan, ar1std=nan, gstd=0.000000, fwhm=0.000000
Writing results
mean
maxvox sig=0F=0atindex 0 0 0seed=1517884366
age
maxvox sig=0F=0atindex 0 0 0seed=1517884366
mri_glmfit done
On Wed, Jan 24, 2018 at 2:59 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
can you send the terminal output of mri_glmfit? On 01/24/2018 02:52 PM, miracle ozzoude wrote: > Hello Doug, > > I looked at the fwhm.dat and fwhm value = 0. I have attached the > mri_glmfit.log file. How do i solve this problem? > > Best, > Paul > > On Mon, Jan 22, 2018 at 11:57 AM, 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: > > If your fwhm is 0, then something is wrong. Look in the fwhm.dat > file in > the glmfit output to see what the value is. Also, send the terminal > output from mri_glmfit (not mri_glmfit-sim) > > > On 01/22/2018 11:43 AM, miracle ozzoude wrote: > > > > ---------- Forwarded message ---------- > > From: *miracle ozzoude* <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>>>> > > Date: Sat, Jan 20, 2018 at 1:56 PM > > Subject: Re: [Freesurfer] monte-carlo error in longitudinal pipeline > > To: Freesurfer support 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>>>> > > > > > > Hello Doug, > > > > I tried using the MC tables that FS distributed. However, i got an > > error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and > > there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are > > my script and cache.mri_glmfi-sim.log files. My FreeSurfer > version is > > stable version 5.3 on mac. Thank you. > > > > Best, > > Paul > > > > mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir > > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache > 3 pos > > --cwpvalthresh 0.05 --2spaces --overwrite > > mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir > > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache > 3 pos > > --cwpvalthresh 0.05 --2spaces --overwrite > > > > On Thu, Jan 18, 2018 at 5:23 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: > > > > Why are you doing your own MC simulation? You can just use the > > tables that we distribute ... > > > > > > On 1/17/18 6:12 PM, miracle ozzoude wrote: > >> Hello Experts, > >> > >> I am running a paired t-test cortical thickness analysis > based on > >> the instruction on the wiki page > >> (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>> > >> <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>>>). > >> However, the monte carlo files weren't not created when i > >> corrected for multiple comparisons. Below are my script, fsgd > >> files, mc-z log file, and a screenshot of contrast folder > missing > >> mc.z maps. Please can you help me figure out why the error is > >> happening. Thank you. > >> > >> Best, > >> Paul > >> > >> *Script*: > >> pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx > >> martrix2=age.mtx > >> #resample each subjects's left and right hemisphere data to > >> fsavarage. > >> mris_preproc --target fsaverage --hemi lh --meas thickness > --out > >> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff > >> mris_preproc --target fsaverage --hemi rh --meas thickness > --out > >> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff > >> # #smoothen the concatenated file by 5mm FWHM. --cortex means > >> only smooth areas in the cortex. N:B. FWHM changes based on > study > >> type. > >> mri_surf2surf --hemi lh --s fsaverage --sval > >> lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval > >> lh.paired-diff.thickness.sm05.mgh > >> mri_surf2surf --hemi rh --s fsaverage --sval > >> rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval > >> rh.paired-diff.thickness.sm05.mgh > >> # #Run GLM analysis > >> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired > >> --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex > --glmdir > >> lh.paired-diff.glmdirir > >> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired > >> --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex > --glmdir > >> rh.paired-diff.glmdir > >> # # #Run Clusterwise correction for multiple comparisons using > >> MONTE CARLO. First create a table for of simulations > >> mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z > 10000 2 > >> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces > --overwrite > >> mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z > 10000 2 > >> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces > --overwrite > >> *Fsgd file 1:pairs.fsgd* > >> > >> GroupDescriptorFile 1 > >> > >> Class ADEX > >> > >> Input 1000_1 ADEX > >> > >> Input 1000_2 ADEX > >> > >> Input 1001_1 ADEX > >> > >> Input 1001_2 ADEX > >> > >> Input 1003_1 ADEX > >> > >> Input 1003_2 ADEX > >> > >> Input 1005_1 ADEX > >> > >> Input 1005_2 ADEX > >> > >> Input 1008_1 ADEX > >> > >> Input 1008_2 ADEX > >> > >> Input 1013_1 ADEX > >> > >> Input 1013_2 ADEX > >> > >> Input 1014_1 ADEX > >> > >> Input 1014_2 ADEX > >> > >> *Fsgd file 2: paired_diff.fsgd* > >> > >> GroupDescriptorFile 1 > >> > >> Class ADEX > >> > >> Variables Age > >> > >> Input 1000 ADEX 72 > >> > >> Input 1001 ADEX 76 > >> > >> Input 1003 ADEX 72 > >> > >> Input 1005 ADEX 80 > >> > >> Input 1008 ADEX 72 > >> > >> Input 1013 ADEX 80 > >> > >> Input 1014 ADEX 80 > >> > >> > >> > >> _______________________________________________ > >> 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. 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 <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
that usually means that something has gone wrong with the analysis. Do the maps look ok? In particular, look at the mask
On 1/20/18 1:56 PM, miracle ozzoude wrote:
Hello Doug,
I tried using the MC tables that FS distributed. However, i got an error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3 on mac. Thank you.
Best, Paul
mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite
On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Why are you doing your own MC simulation? You can just use the tables that we distribute ... On 1/17/18 6:12 PM, miracle ozzoude wrote:Hello Experts, I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you. Best, Paul *Script*: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx #resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh # #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite *Fsgd file 1:pairs.fsgd* GroupDescriptorFile 1 Class ADEX Input 1000_1 ADEX Input 1000_2 ADEX Input 1001_1 ADEX Input 1001_2 ADEX Input 1003_1 ADEX Input 1003_2 ADEX Input 1005_1 ADEX Input 1005_2 ADEX Input 1008_1 ADEX Input 1008_2 ADEX Input 1013_1 ADEX Input 1013_2 ADEX Input 1014_1 ADEX Input 1014_2 ADEX *Fsgd file 2: paired_diff.fsgd* GroupDescriptorFile 1 Class ADEX Variables Age Input 1000 ADEX 72 Input 1001 ADEX 76 Input 1003 ADEX 72 Input 1005 ADEX 80 Input 1008 ADEX 72 Input 1013 ADEX 80 Input 1014 ADEX 80 _______________________________________________ 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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Hello Doug,
I have attached a screen shot of the mask.mgh for both right and left hemispheres. Everything looks yellow. I followed the paired t-test tutorial on the wiki page (included my scripts, fsgd files, and matrix in email thread). How do i go about fixing it? Thanks you
Best, Paul
On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
that usually means that something has gone wrong with the analysis. Do the maps look ok? In particular, look at the mask
On 1/20/18 1:56 PM, miracle ozzoude wrote:
Hello Doug,
I tried using the MC tables that FS distributed. However, i got an error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3 on mac. Thank you.
Best, Paul
mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite
On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Why are you doing your own MC simulation? You can just use the tables that we distribute ...
On 1/17/18 6:12 PM, miracle ozzoude wrote:
Hello Experts,
I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page (https://surfer.nmr.mgh.harvar d.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you.
Best, Paul
*Script*: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx #resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh # #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite *Fsgd file 1:pairs.fsgd*
GroupDescriptorFile 1
Class ADEX
Input 1000_1 ADEX
Input 1000_2 ADEX
Input 1001_1 ADEX
Input 1001_2 ADEX
Input 1003_1 ADEX
Input 1003_2 ADEX
Input 1005_1 ADEX
Input 1005_2 ADEX
Input 1008_1 ADEX
Input 1008_2 ADEX
Input 1013_1 ADEX
Input 1013_2 ADEX
Input 1014_1 ADEX
Input 1014_2 ADEX *Fsgd file 2: paired_diff.fsgd*
GroupDescriptorFile 1
Class ADEX
Variables Age
Input 1000 ADEX 72
Input 1001 ADEX 76
Input 1003 ADEX 72
Input 1005 ADEX 80
Input 1008 ADEX 72
Input 1013 ADEX 80
Input 1014 ADEX 80
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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.
Can you upload the glmfit folders and the glmfit input (--y file) to our filedrop?
https://gate.nmr.mgh.harvard.edu/filedrop2/
On 2/1/18 7:46 PM, miracle ozzoude wrote:
Hello Doug,
I have attached a screen shot of the mask.mgh for both right and left hemispheres. Everything looks yellow. I followed the paired t-test tutorial on the wiki page (included my scripts, fsgd files, and matrix in email thread). How do i go about fixing it? Thanks you
Best, Paul
On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
that usually means that something has gone wrong with the analysis. Do the maps look ok? In particular, look at the mask On 1/20/18 1:56 PM, miracle ozzoude wrote:Hello Doug, I tried using the MC tables that FS distributed. However, i got an error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3 on mac. Thank you. Best, Paul mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Why are you doing your own MC simulation? You can just use the tables that we distribute ... On 1/17/18 6:12 PM, miracle ozzoude wrote:Hello Experts, I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you. Best, Paul *Script*: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx #resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh # #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite *Fsgd file 1:pairs.fsgd* GroupDescriptorFile 1 Class ADEX Input 1000_1 ADEX Input 1000_2 ADEX Input 1001_1 ADEX Input 1001_2 ADEX Input 1003_1 ADEX Input 1003_2 ADEX Input 1005_1 ADEX Input 1005_2 ADEX Input 1008_1 ADEX Input 1008_2 ADEX Input 1013_1 ADEX Input 1013_2 ADEX Input 1014_1 ADEX Input 1014_2 ADEX *Fsgd file 2: paired_diff.fsgd* GroupDescriptorFile 1 Class ADEX Variables Age Input 1000 ADEX 72 Input 1001 ADEX 76 Input 1003 ADEX 72 Input 1005 ADEX 80 Input 1008 ADEX 72 Input 1013 ADEX 80 Input 1014 ADEX 80 _______________________________________________ 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 <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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Hello Doug,
I have uploaded the files you requested. Thank you for your help.
Best, Paul
On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Can you upload the glmfit folders and the glmfit input (--y file) to our filedrop?
https://gate.nmr.mgh.harvard.edu/filedrop2/
On 2/1/18 7:46 PM, miracle ozzoude wrote:
Hello Doug,
I have attached a screen shot of the mask.mgh for both right and left hemispheres. Everything looks yellow. I followed the paired t-test tutorial on the wiki page (included my scripts, fsgd files, and matrix in email thread). How do i go about fixing it? Thanks you
Best, Paul
On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
that usually means that something has gone wrong with the analysis. Do the maps look ok? In particular, look at the mask
On 1/20/18 1:56 PM, miracle ozzoude wrote:
Hello Doug,
I tried using the MC tables that FS distributed. However, i got an error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3 on mac. Thank you.
Best, Paul
mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite
On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
Why are you doing your own MC simulation? You can just use the tables that we distribute ...
On 1/17/18 6:12 PM, miracle ozzoude wrote:
Hello Experts,
I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page (https://surfer.nmr.mgh.harvar d.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you.
Best, Paul
*Script*: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx #resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh # #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite *Fsgd file 1:pairs.fsgd*
GroupDescriptorFile 1
Class ADEX
Input 1000_1 ADEX
Input 1000_2 ADEX
Input 1001_1 ADEX
Input 1001_2 ADEX
Input 1003_1 ADEX
Input 1003_2 ADEX
Input 1005_1 ADEX
Input 1005_2 ADEX
Input 1008_1 ADEX
Input 1008_2 ADEX
Input 1013_1 ADEX
Input 1013_2 ADEX
Input 1014_1 ADEX
Input 1014_2 ADEX *Fsgd file 2: paired_diff.fsgd*
GroupDescriptorFile 1
Class ADEX
Variables Age
Input 1000 ADEX 72
Input 1001 ADEX 76
Input 1003 ADEX 72
Input 1005 ADEX 80
Input 1008 ADEX 72
Input 1013 ADEX 80
Input 1014 ADEX 80
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
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
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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.
The first frame in your input file is all 0s, so something is wrong with the fist subject
On 2/3/18 3:03 PM, miracle ozzoude wrote:
Hello Doug,
I have uploaded the files you requested. Thank you for your help.
Best, Paul
On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you upload the glmfit folders and the glmfit input (--y file) to our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2/ <https://gate.nmr.mgh.harvard.edu/filedrop2/> On 2/1/18 7:46 PM, miracle ozzoude wrote:Hello Doug, I have attached a screen shot of the mask.mgh for both right and left hemispheres. Everything looks yellow. I followed the paired t-test tutorial on the wiki page (included my scripts, fsgd files, and matrix in email thread). How do i go about fixing it? Thanks you Best, Paul On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: that usually means that something has gone wrong with the analysis. Do the maps look ok? In particular, look at the mask On 1/20/18 1:56 PM, miracle ozzoude wrote:Hello Doug, I tried using the MC tables that FS distributed. However, i got an error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3 on mac. Thank you. Best, Paul mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Why are you doing your own MC simulation? You can just use the tables that we distribute ... On 1/17/18 6:12 PM, miracle ozzoude wrote:Hello Experts, I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you. Best, Paul *Script*: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx #resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh # #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite *Fsgd file 1:pairs.fsgd* GroupDescriptorFile 1 Class ADEX Input 1000_1 ADEX Input 1000_2 ADEX Input 1001_1 ADEX Input 1001_2 ADEX Input 1003_1 ADEX Input 1003_2 ADEX Input 1005_1 ADEX Input 1005_2 ADEX Input 1008_1 ADEX Input 1008_2 ADEX Input 1013_1 ADEX Input 1013_2 ADEX Input 1014_1 ADEX Input 1014_2 ADEX *Fsgd file 2: paired_diff.fsgd* GroupDescriptorFile 1 Class ADEX Variables Age Input 1000 ADEX 72 Input 1001 ADEX 76 Input 1003 ADEX 72 Input 1005 ADEX 80 Input 1008 ADEX 72 Input 1013 ADEX 80 Input 1014 ADEX 80 _______________________________________________ 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. 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Hello Doug,
Thank you. How do i got about fixing? Do you think it's a good idea to start afresh on this subject (i.e. recon-all and longitudinal pipeline)?
Best, Paul
On Mon, Feb 5, 2018 at 12:20 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
The first frame in your input file is all 0s, so something is wrong with the fist subject
On 2/3/18 3:03 PM, miracle ozzoude wrote:
Hello Doug,
I have uploaded the files you requested. Thank you for your help.
Best, Paul
On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Can you upload the glmfit folders and the glmfit input (--y file) to our filedrop?
https://gate.nmr.mgh.harvard.edu/filedrop2/
On 2/1/18 7:46 PM, miracle ozzoude wrote:
Hello Doug,
I have attached a screen shot of the mask.mgh for both right and left hemispheres. Everything looks yellow. I followed the paired t-test tutorial on the wiki page (included my scripts, fsgd files, and matrix in email thread). How do i go about fixing it? Thanks you
Best, Paul
On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
that usually means that something has gone wrong with the analysis. Do the maps look ok? In particular, look at the mask
On 1/20/18 1:56 PM, miracle ozzoude wrote:
Hello Doug,
I tried using the MC tables that FS distributed. However, i got an error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3 on mac. Thank you.
Best, Paul
mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite
On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve < greve@nmr.mgh.harvard.edu> wrote:
Why are you doing your own MC simulation? You can just use the tables that we distribute ...
On 1/17/18 6:12 PM, miracle ozzoude wrote:
Hello Experts,
I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page (https://surfer.nmr.mgh.harvar d.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you.
Best, Paul
*Script*: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx #resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh # #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite *Fsgd file 1:pairs.fsgd*
GroupDescriptorFile 1
Class ADEX
Input 1000_1 ADEX
Input 1000_2 ADEX
Input 1001_1 ADEX
Input 1001_2 ADEX
Input 1003_1 ADEX
Input 1003_2 ADEX
Input 1005_1 ADEX
Input 1005_2 ADEX
Input 1008_1 ADEX
Input 1008_2 ADEX
Input 1013_1 ADEX
Input 1013_2 ADEX
Input 1014_1 ADEX
Input 1014_2 ADEX *Fsgd file 2: paired_diff.fsgd*
GroupDescriptorFile 1
Class ADEX
Variables Age
Input 1000 ADEX 72
Input 1001 ADEX 76
Input 1003 ADEX 72
Input 1005 ADEX 80
Input 1008 ADEX 72
Input 1013 ADEX 80
Input 1014 ADEX 80
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I don't know, you'll have to look at how you computed the first frame. Maybe the 1st and 2nd time point for that subject are the same
On 02/05/2018 04:27 PM, miracle ozzoude wrote:
Hello Doug,
Thank you. How do i got about fixing? Do you think it's a good idea to start afresh on this subject (i.e. recon-all and longitudinal pipeline)?
Best, Paul
On Mon, Feb 5, 2018 at 12:20 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The first frame in your input file is all 0s, so something is wrong with the fist subject On 2/3/18 3:03 PM, miracle ozzoude wrote:Hello Doug, I have uploaded the files you requested. Thank you for your help. Best, Paul On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Can you upload the glmfit folders and the glmfit input (--y file) to our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2/ <https://gate.nmr.mgh.harvard.edu/filedrop2/> On 2/1/18 7:46 PM, miracle ozzoude wrote:Hello Doug, I have attached a screen shot of the mask.mgh for both right and left hemispheres. Everything looks yellow. I followed the paired t-test tutorial on the wiki page (included my scripts, fsgd files, and matrix in email thread). How do i go about fixing it? Thanks you Best, Paul On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: that usually means that something has gone wrong with the analysis. Do the maps look ok? In particular, look at the mask On 1/20/18 1:56 PM, miracle ozzoude wrote:Hello Doug, I tried using the MC tables that FS distributed. However, i got an error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3 on mac. Thank you. Best, Paul mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Why are you doing your own MC simulation? You can just use the tables that we distribute ... On 1/17/18 6:12 PM, miracle ozzoude wrote:Hello Experts, I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z maps. Please can you help me figure out why the error is happening. Thank you. Best, Paul *Script*: pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx #resample each subjects's left and right hemisphere data to fsavarage. mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type. mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh # #Run GLM analysis mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite *Fsgd file 1:pairs.fsgd* GroupDescriptorFile 1 Class ADEX Input 1000_1 ADEX Input 1000_2 ADEX Input 1001_1 ADEX Input 1001_2 ADEX Input 1003_1 ADEX Input 1003_2 ADEX Input 1005_1 ADEX Input 1005_2 ADEX Input 1008_1 ADEX Input 1008_2 ADEX Input 1013_1 ADEX Input 1013_2 ADEX Input 1014_1 ADEX Input 1014_2 ADEX *Fsgd file 2: paired_diff.fsgd* GroupDescriptorFile 1 Class ADEX Variables Age Input 1000 ADEX 72 Input 1001 ADEX 76 Input 1003 ADEX 72 Input 1005 ADEX 80 Input 1008 ADEX 72 Input 1013 ADEX 80 Input 1014 ADEX 80 _______________________________________________ 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. 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Douglas Greve -
Douglas N Greve
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miracle ozzoude