Re: [Freesurfer] calculating spc on lobes annotation in longitudinal structural analysis
The Freesurfer version we have installed is 5.1.0 if that helps.
Best,
Jeremy
---
Dear all,
I'm trying to get thickness spc stats for the individual lobe labels
(specifically the frontal lobe) I created per subject per time point (in
subject's longitudinal analysis template space) using:
mri_annotation2label --subject $i --hemi ?h --lobesStrict ?h.lobes
I've run mris_anatomical_stats to get out the stats and put them in each
subject and time point's stats folder:
mris_anatomical_stats -a lobes.annot -f $i/stats/lh.lobes.stats $i ?h
Now I'm trying to calculate the spc using:
long_stats_slopes --qdec long.qdec.table.dat --stats lh.lobes --meas
thickness --do-spc --time years --out-spc lh.spc.lobes.txt
but I'm getting an error (it works when I use the regular aparc and aseg
stats files though). Here's my output:
---
Parsing the qdec table: long.qdec.table.dat
Working in SUBJECTS_DIR: /home/j/jy/jy72/scratch/AE/FSstruct/
Subject-Template: CISC4962plate
INFO: 2 TPs in CISC4962plate , mean age: 0.565
aparcstats2table --common-parcs --hemi lh --parc lobes --subjects
CISC4962.long.CISC4962plate CISC4962-2.long.CISC4962plate --meas
thickness --tablefile
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat
-d space
SUBJECTS_DIR : /home/j/jy/jy72/scratch/AE/FSstruct/
Parsing the .stats files
Building the table..
Writing the table to
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat
Writing ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat ...
mri_glmfit --table
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat
--X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat
--allow-zero-dof --no-contrasts-ok --glmdir
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm
$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
cwd /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec
cmdline mri_glmfit --table
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat
--X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat
--allow-zero-dof --no-contrasts-ok --glmdir
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm
sysname Linux
hostname apollo-login
machine x86_64
user jy72
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat
logyflag 0
X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat
usedti 0
glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm
Loading y from
/mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat
Found 6 data colums
Found 2 data rows
Saving design matrix to
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/Xg.dat
Normalized matrix condition is 1
Matrix condition is 1.76991
search space = 6.000000
DOF = 0
Starting fit and test
Fit completed in 0 minutes
Writing results
lh.lobes.thickness
lh_frontal_thickness
lh_cingulate_thickness
lh_occipital_thickness
lh_temporal_thickness
lh_parietal_thickness
lh_insula_thickness
mri_glmfit done
mri_convert --frame 0
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh
mri_convert --frame 0
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
keeping frame 0
writing to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh...
mri_convert --frame 1
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh
mri_convert --frame 1
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
keeping frame 1
writing to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh...
mris_calc -o
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-spc.dat.mgh
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh div
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh
ERROR: mris_calc compute sym. pct. change (spc) problem?
---
Am I missing a step somewhere when trying to do this? Please help.
Thanks!
Jeremy
--
Jeremy Young
PhD Researcher
Behavioural and Clinical Neuroscience
School of Psychology
University of Sussex
Brighton
BN1 9QH
01273 872776
J.Young at sussex.ac.ukhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
What is spc? doug
On 02/04/2014 07:18 AM, Jeremy Young wrote:
The Freesurfer version we have installed is 5.1.0 if that helps.
Best, Jeremy
Dear all,
I'm trying to get thickness spc stats for the individual lobe labels (specifically the frontal lobe) I created per subject per time point (in subject's longitudinal analysis template space) using: mri_annotation2label --subject $i --hemi ?h --lobesStrict ?h.lobes
I've run mris_anatomical_stats to get out the stats and put them in each subject and time point's stats folder: mris_anatomical_stats -a lobes.annot -f $i/stats/lh.lobes.stats $i ?h
Now I'm trying to calculate the spc using: long_stats_slopes --qdec long.qdec.table.dat --stats lh.lobes --meas thickness --do-spc --time years --out-spc lh.spc.lobes.txt
but I'm getting an error (it works when I use the regular aparc and aseg stats files though). Here's my output:
Parsing the qdec table: long.qdec.table.dat
Working in SUBJECTS_DIR: /home/j/jy/jy72/scratch/AE/FSstruct/
Subject-Template: CISC4962plate
INFO: 2 TPs in CISC4962plate , mean age: 0.565
aparcstats2table --common-parcs --hemi lh --parc lobes --subjects CISC4962.long.CISC4962plate CISC4962-2.long.CISC4962plate --meas thickness --tablefile ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat -d space
SUBJECTS_DIR : /home/j/jy/jy72/scratch/AE/FSstruct/ Parsing the .stats files Building the table.. Writing the table to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat
Writing ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat ...
mri_glmfit --table ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat --X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat --allow-zero-dof --no-contrasts-ok --glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm
$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec cmdline mri_glmfit --table ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat --X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat --allow-zero-dof --no-contrasts-ok --glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm sysname Linux hostname apollo-login machine x86_64 user jy72 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat logyflag 0 X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat usedti 0 glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm Loading y from /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat Found 6 data colums Found 2 data rows Saving design matrix to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/Xg.dat Normalized matrix condition is 1 Matrix condition is 1.76991 search space = 6.000000 DOF = 0 Starting fit and test Fit completed in 0 minutes Writing results lh.lobes.thickness lh_frontal_thickness lh_cingulate_thickness lh_occipital_thickness lh_temporal_thickness lh_parietal_thickness lh_insula_thickness mri_glmfit done
mri_convert --frame 0 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh
mri_convert --frame 0 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh...
mri_convert --frame 1 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh
mri_convert --frame 1 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 1 writing to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh...
mris_calc -o ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-spc.dat.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh div ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh
ERROR: mris_calc compute sym. pct. change (spc) problem?
Am I missing a step somewhere when trying to do this? Please help.
Thanks! Jeremy
-- Jeremy Young PhD Researcher Behavioural and Clinical Neuroscience School of Psychology University of Sussex Brighton BN1 9QH 01273 872776 J.Young at sussex.ac.uk 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
Sorry seems like my reply didn't go through to the list. Still trying to figure this out if anyone has some ideas on what to do / recommend trying to calculate manually.
Best, Jeremy
-----Original Message----- From: Jeremy Young Sent: Tuesday, February 04, 2014 4:30 PM To: 'Douglas N Greve' Subject: RE: [Freesurfer] calculating spc on lobes annotation in longitudinal structural analysis
Hi Doug,
It's the symmetrized percent change, it's the rate of change divided by the average thickness between time points; it's the recommended parameter to use according to the longitudinal analysis tutorial (instead of just percent change relative to time point 1).
Thanks! Jeremy
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, February 04, 2014 4:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] calculating spc on lobes annotation in longitudinal structural analysis
What is spc? doug
On 02/04/2014 07:18 AM, Jeremy Young wrote:
The Freesurfer version we have installed is 5.1.0 if that helps.
Best, Jeremy
Dear all,
I'm trying to get thickness spc stats for the individual lobe labels (specifically the frontal lobe) I created per subject per time point (in subject's longitudinal analysis template space) using: mri_annotation2label --subject $i --hemi ?h --lobesStrict ?h.lobes
I've run mris_anatomical_stats to get out the stats and put them in each subject and time point's stats folder: mris_anatomical_stats -a lobes.annot -f $i/stats/lh.lobes.stats $i ?h
Now I'm trying to calculate the spc using: long_stats_slopes --qdec long.qdec.table.dat --stats lh.lobes --meas thickness --do-spc --time years --out-spc lh.spc.lobes.txt
but I'm getting an error (it works when I use the regular aparc and aseg stats files though). Here's my output:
Parsing the qdec table: long.qdec.table.dat
Working in SUBJECTS_DIR: /home/j/jy/jy72/scratch/AE/FSstruct/
Subject-Template: CISC4962plate
INFO: 2 TPs in CISC4962plate , mean age: 0.565
aparcstats2table --common-parcs --hemi lh --parc lobes --subjects CISC4962.long.CISC4962plate CISC4962-2.long.CISC4962plate --meas thickness --tablefile ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness- stack.dat -d space
SUBJECTS_DIR : /home/j/jy/jy72/scratch/AE/FSstruct/ Parsing the .stats files Building the table.. Writing the table to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness- stack.dat
Writing ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat ...
mri_glmfit --table ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness- stack.dat --X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat --allow-zero-dof --no-contrasts-ok --glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm
$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec cmdline mri_glmfit --table ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness- stack.dat --X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat --allow-zero-dof --no-contrasts-ok --glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm sysname Linux hostname apollo-login machine x86_64 user jy72 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes _thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat logyflag 0 X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat usedti 0 glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm Loading y from /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes _thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat Found 6 data colums Found 2 data rows Saving design matrix to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/Xg.dat Normalized matrix condition is 1 Matrix condition is 1.76991 search space = 6.000000 DOF = 0 Starting fit and test Fit completed in 0 minutes Writing results lh.lobes.thickness lh_frontal_thickness lh_cingulate_thickness lh_occipital_thickness lh_temporal_thickness lh_parietal_thickness lh_insula_thickness mri_glmfit done
mri_convert --frame 0 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh
mri_convert --frame 0 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh...
mri_convert --frame 1 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh
mri_convert --frame 1 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 1 writing to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh...
mris_calc -o ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness- spc.dat.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh div ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh
ERROR: mris_calc compute sym. pct. change (spc) problem?
Am I missing a step somewhere when trying to do this? Please help.
Thanks! Jeremy
-- Jeremy Young PhD Researcher Behavioural and Clinical Neuroscience School of Psychology University of Sussex Brighton BN1 9QH 01273 872776 J.Young at sussex.ac.uk https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Hi Jeremy,
sorry, did not see your email earlier. I am not sure what is going on though. I have done this type of analysis before and it worked for me. I remember there were a few bugs (with long file names etc see release notes: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes ) in the mris_calc tool which is called from my script.
You should try to replace the mris_calc with a new version, there is a link to a fixed version on the release notes.
Or update to FreeSurfer 5.3 ;-)
Best, Martin
On 02/06/2014 08:38 AM, Jeremy Young wrote:
Sorry seems like my reply didn't go through to the list. Still trying to figure this out if anyone has some ideas on what to do / recommend trying to calculate manually.
Best, Jeremy
-----Original Message----- From: Jeremy Young Sent: Tuesday, February 04, 2014 4:30 PM To: 'Douglas N Greve' Subject: RE: [Freesurfer] calculating spc on lobes annotation in longitudinal structural analysis
Hi Doug,
It's the symmetrized percent change, it's the rate of change divided by the average thickness between time points; it's the recommended parameter to use according to the longitudinal analysis tutorial (instead of just percent change relative to time point 1).
Thanks! Jeremy
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, February 04, 2014 4:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] calculating spc on lobes annotation in longitudinal structural analysis
What is spc? doug
On 02/04/2014 07:18 AM, Jeremy Young wrote:
The Freesurfer version we have installed is 5.1.0 if that helps.
Best, Jeremy
Dear all,
I'm trying to get thickness spc stats for the individual lobe labels (specifically the frontal lobe) I created per subject per time point (in subject's longitudinal analysis template space) using: mri_annotation2label --subject $i --hemi ?h --lobesStrict ?h.lobes
I've run mris_anatomical_stats to get out the stats and put them in each subject and time point's stats folder: mris_anatomical_stats -a lobes.annot -f $i/stats/lh.lobes.stats $i ?h
Now I'm trying to calculate the spc using: long_stats_slopes --qdec long.qdec.table.dat --stats lh.lobes --meas thickness --do-spc --time years --out-spc lh.spc.lobes.txt
but I'm getting an error (it works when I use the regular aparc and aseg stats files though). Here's my output:
Parsing the qdec table: long.qdec.table.dat
Working in SUBJECTS_DIR: /home/j/jy/jy72/scratch/AE/FSstruct/
Subject-Template: CISC4962plate
INFO: 2 TPs in CISC4962plate , mean age: 0.565
aparcstats2table --common-parcs --hemi lh --parc lobes --subjects CISC4962.long.CISC4962plate CISC4962-2.long.CISC4962plate --meas thickness --tablefile ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness- stack.dat -d space
SUBJECTS_DIR : /home/j/jy/jy72/scratch/AE/FSstruct/ Parsing the .stats files Building the table.. Writing the table to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness- stack.dat
Writing ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat ...
mri_glmfit --table ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness- stack.dat --X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat --allow-zero-dof --no-contrasts-ok --glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm
$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec cmdline mri_glmfit --table ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness- stack.dat --X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat --allow-zero-dof --no-contrasts-ok --glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm sysname Linux hostname apollo-login machine x86_64 user jy72 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes _thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat logyflag 0 X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat usedti 0 glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm Loading y from /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes _thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat Found 6 data colums Found 2 data rows Saving design matrix to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/Xg.dat Normalized matrix condition is 1 Matrix condition is 1.76991 search space = 6.000000 DOF = 0 Starting fit and test Fit completed in 0 minutes Writing results lh.lobes.thickness lh_frontal_thickness lh_cingulate_thickness lh_occipital_thickness lh_temporal_thickness lh_parietal_thickness lh_insula_thickness mri_glmfit done
mri_convert --frame 0 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh
mri_convert --frame 0 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh...
mri_convert --frame 1 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh
mri_convert --frame 1 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 1 writing to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh...
mris_calc -o ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness- spc.dat.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh div ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh
ERROR: mris_calc compute sym. pct. change (spc) problem?
Am I missing a step somewhere when trying to do this? Please help.
Thanks! Jeremy
-- Jeremy Young PhD Researcher Behavioural and Clinical Neuroscience School of Psychology University of Sussex Brighton BN1 9QH 01273 872776 J.Young at sussex.ac.uk https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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