I've attached it for you as a .txt file
----- Ursprüngliche Mail -----
Von: "Douglas N Greve" <[email protected]>
An: [email protected]
Gesendet: Dienstag, 21. Februar 2017 17:47:23
Betreff: Re: [Freesurfer] cluster as ROI
Can you send the terminal output?
On 02/21/2017 11:44 AM, Clara Kühn wrote:
> Hm. I already did that. In none of my glmdirs are files like the
> csdbase.sig.ocn.mgh. This is the mri_glmfit-sim that I ran:
>
> mri_glmfir-sim --glmdir $SUBJECTS_DIR/qdec/40kids-rh-area-spc --cache-dir
> $SUBJECTS_DIR/average/multi-comp-cor/ --cache 3.0 abs --cwp 0.05 --2spaces
>
> Cheers Clara
>
> ----- Ursprüngliche Mail -----
> Von: "Douglas N Greve" <[email protected]>
> An: [email protected]
> Gesendet: Dienstag, 21. Februar 2017 17:24:02
> Betreff: Re: [Freesurfer] cluster as ROI
>
> You will have to run mri_glmfit-sim
>
>
> On 02/21/2017 04:07 AM, Clara Kühn wrote:
>> Hi Doug,
>>
>> I have a gamma.mgh file in glmdir/rh-Diff-1-3-Intercept-long.area-spc/ and I
>> also have a contrasts.sig.mgh file in the gmldir.
>>
>> Could either of these be used instead of csdbase.sig.ocn.mgh? Or how could I
>> retrieve this file?
>>
>> Thanks for your help!
>> Clara
>>
>> ----- Ursprüngliche Mail -----
>> Von: "Douglas N Greve" <[email protected]>
>> An: [email protected]
>> Gesendet: Donnerstag, 16. Februar 2017 19:22:01
>> Betreff: Re: [Freesurfer] cluster as ROI
>>
>> On 02/16/2017 04:24 AM, Clara Kühn wrote:
>>> Hi Doug,
>>>
>>> thanks for your input. Could you specify some of the flags for me?
>>>
>>> --i tp1.stack.mgh - is this supposed to be the cluster or file in my
>>> /template/surf/ folder that I get from mris_preproc and mris_surf2surf?
>> input from preproc/surf2surf
>>> --seg glmdir/contrast/csdbase.sig.ocn.mgh - I don't seem to have this file.
>>> The only files I have in the contrast folder are 2 .mat files
>> there should be a bunch of output there from mri_glmfit and
>> mri_glmfit-sim. Actually, if you ran qdec, then the glmfit-sim output
>> may not be there. you'll have to run it separately. But there should be,
>> eg, gamma.mgh there
>>> Cheers
>>> Clara
>>>
>>> ----- Ursprüngliche Mail -----
>>> Von: "Douglas N Greve" <[email protected]>
>>> An: [email protected]
>>> Gesendet: Mittwoch, 15. Februar 2017 23:35:54
>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>
>>> Use something like this
>>>
>>> mri_segstats --i tp1.stack.mgh --seg glmdir/contrast/csdbase.sig.ocn.mgh
>>> --excludeid 0 --avgwf tp1.clustermean.dat
>>>
>>> The output tp1.clustermean.dat will be a matrix with nsubjects rows and
>>> nclusters columns where the value represents the mean for that subject
>>> in that cluster.
>>>
>>>
>>>
>>> On 02/14/2017 11:47 AM, Clara Kühn wrote:
>>>> Dear FreeSurfer Experts,
>>>>
>>>> I compared 2 groups in QDEC in spc (from pre to post) and found a cluster
>>>> that survives Monte Carlo correction. Now I would like to extract the data
>>>> for each participant and each time point from that cluster so that I can
>>>> plot the change.
>>>>
>>>> How could I do this? I tried this so far:
>>>> aparcstats2table --qdec-long $SUBJECTS
>>>> DIR/qdec/2016.12.06-40kids-long.qdec.table2-1.dat --hemi rh - -tablefile
>>>> $SUBJECTS
>>>> DIR/qdec/2016.12.08-40kids-2stagemodel/rharea-cluster-extracted.txt --parc
>>>> $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rh-area
>>>> again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
>>>>
>>>> But I get this error:
>>>> ERROR: The stats file
>>>> /nobackup/etsch2/kids/prepost-61kids/AL3K_1.long.AL3K.base/stats/rh./nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh.stats
>>>> is not found or is too small to be a valid statsfile
>>>> Use --skip flag to automatically skip bad stats files
>>>>
>>>>
>>>> Do I have to define my cluster as a ROI and then warp it onto the single
>>>> time points? How would I do that?
>>>>
>>>> Any help is much appreciated!
>>>> Thank you
>>>>
>>>> Clara
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[email protected]
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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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
mri_glmfit-sim --glmdir
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again/
--cache-dir /nobackup/etsch2/kids/prepost-61kids//average/mult-comp-cor/
--cache 3.0 abs --cwp 0.05 --2spaces
cmdline mri_glmfit --y /nobackup/etsch2/kids/prepost-61kids/qdec/Untitled/y.mgh
--fsgd /nobackup/etsch2/kids/prepost-61kids/qdec/Untitled/qdec.fsgd dods
--glmdir /nobackup/etsch2/kids/prepost-61kids/qdec/Untitled --surf
81kids_template rh --C
/nobackup/etsch2/kids/prepost-61kids/qdec/Untitled/contrasts/rh-Avg-Intercept-long.area-spc.mat
--C
/nobackup/etsch2/kids/prepost-61kids/qdec/Untitled/contrasts/rh-Diff-1-3-Intercept-long.area-spc.mat
SURFACE: 81kids_template rh
log file is
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//cache.mri_glmfit-sim.log
cd /home/raid2/ckuehn
/afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/bin/mri_glmfit-sim
--glmdir
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again/
--cache-dir /nobackup/etsch2/kids/prepost-61kids//average/mult-comp-cor/
--cache 3.0 abs --cwp 0.05 --2spaces
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Tue Feb 21 17:52:29 CET 2017
Linux etsch 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 x86_64
x86_64 x86_64 GNU/Linux
ckuehn
setenv SUBJECTS_DIR /nobackup/etsch2/kids/prepost-61kids/
FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64
Original mri_glmfit command line:
cmdline mri_glmfit --y /nobackup/etsch2/kids/prepost-61kids/qdec/Untitled/y.mgh
--fsgd /nobackup/etsch2/kids/prepost-61kids/qdec/Untitled/qdec.fsgd dods
--glmdir /nobackup/etsch2/kids/prepost-61kids/qdec/Untitled --surf
81kids_template rh --C
/nobackup/etsch2/kids/prepost-61kids/qdec/Untitled/contrasts/rh-Avg-Intercept-long.area-spc.mat
--C
/nobackup/etsch2/kids/prepost-61kids/qdec/Untitled/contrasts/rh-Diff-1-3-Intercept-long.area-spc.mat
DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 8.390561
CSD
/nobackup/etsch2/kids/prepost-61kids//average/mult-comp-cor//81kids_template/rh/cortex/fwhm08/abs/th30/mc-z.csd
mri_surfcluster --in
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/sig.mgh
--csd
/nobackup/etsch2/kids/prepost-61kids//average/mult-comp-cor//81kids_template/rh/cortex/fwhm08/abs/th30/mc-z.csd
--mask
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//mask.mgh
--cwsig
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
--vwsig
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.voxel.mgh
--sum
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.cluster.summary
--ocn
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
--oannot
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.ocn.annot
--annot aparc --csdpdf
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.pdf.dat
--cwpvalthresh 0.05 --o
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.masked.mgh
--no-fixmni --bonferroni 2 --surf white
Creating CDFs from CSD files
csd->threshsign = 0
thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
hemi = rh
srcid =
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/sig.mgh
srcsubjid = 81kids_template
srcsurf = white
srcframe = 0
thsign = abs
thmin = 3
thmax = -1
fdr = -1
minarea = 0
Bonferroni = 2
xfmfile = talairach.xfm
nth = -1
outid =
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.masked.mgh
MGH
ocnid =
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
MGH
sumfile =
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.cluster.summary
subjectsdir = /nobackup/etsch2/kids/prepost-61kids/
FixMNI = 0
Found 89846 vertices in mask
Found 89846 vertices in mask
Found 89846 points in clabel.
------------- XFM matrix (RAS2RAS) ---------------
/nobackup/etsch2/kids/prepost-61kids//81kids_template/mri/transforms/talairach.xfm
1.179 -0.002 -0.020 5.339;
-0.003 1.244 -0.111 -14.198;
0.028 0.025 1.307 -11.932;
0.000 0.000 0.000 1.000;
----------------------------------------------------
Reading source surface
/nobackup/etsch2/kids/prepost-61kids//81kids_template/surf/rh.white
Done reading source surface
Reading annotation
/nobackup/etsch2/kids/prepost-61kids//81kids_template/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Computing metric properties
Loading source values
number of voxels in search space = 89846
Done loading source values (nvtxs = 98497)
overall max = 3.11852 at vertex 5647
overall min = -4.11048 at vertex 49987
surface nvertices 98497
surface area 67948.492188
surface area 67948.421875
Computing voxel-wise significance
CSDpvalMaxSigMap(): found 109/98497 above 0
NOT Adjusting threshold for 1-tailed test
Searching for Clusters ...
thmin=3.000000 (3.000000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000
Found 6 clusters
Max cluster size 20.754253
Pruning by CW P-Value 0.05
Saving thresholded output to
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.masked.mgh
Saving cluster numbers to
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
Saving cluster pval
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
Constructing output annotation
Writing annotation
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.ocn.annot
mri_segstats --seg
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
--exclude 0 --i
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//y.mgh
--avgwf
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.y.ocn.dat
--sum /tmp/mri_glmfit-sim.junk.658856
$Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $
cwd
cmdline mri_segstats --seg
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
--exclude 0 --i
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//y.mgh
--avgwf
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.y.ocn.dat
--sum /tmp/mri_glmfit-sim.junk.658856
sysname Linux
hostname etsch
machine x86_64
user ckuehn
UseRobust 0
Loading
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
Loading
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//y.mgh
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 0 segmentations
Computing spatial average of each frame
Writing to
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.y.ocn.dat
mri_segstats done
mri_convert
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
--frame 0
mri_convert
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
--frame 0
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
keeping frame 0
writing to
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Avg-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh...
mri_surfcluster --in
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/sig.mgh
--csd
/nobackup/etsch2/kids/prepost-61kids//average/mult-comp-cor//81kids_template/rh/cortex/fwhm08/abs/th30/mc-z.csd
--mask
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//mask.mgh
--cwsig
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
--vwsig
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.voxel.mgh
--sum
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.summary
--ocn
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
--oannot
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.annot
--annot aparc --csdpdf
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.pdf.dat
--cwpvalthresh 0.05 --o
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.masked.mgh
--no-fixmni --bonferroni 2 --surf white
Creating CDFs from CSD files
csd->threshsign = 0
thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
hemi = rh
srcid =
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/sig.mgh
srcsubjid = 81kids_template
srcsurf = white
srcframe = 0
thsign = abs
thmin = 3
thmax = -1
fdr = -1
minarea = 0
Bonferroni = 2
xfmfile = talairach.xfm
nth = -1
outid =
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.masked.mgh
MGH
ocnid =
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
MGH
sumfile =
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.summary
subjectsdir = /nobackup/etsch2/kids/prepost-61kids/
FixMNI = 0
Found 89846 vertices in mask
Found 89846 vertices in mask
Found 89846 points in clabel.
------------- XFM matrix (RAS2RAS) ---------------
/nobackup/etsch2/kids/prepost-61kids//81kids_template/mri/transforms/talairach.xfm
1.179 -0.002 -0.020 5.339;
-0.003 1.244 -0.111 -14.198;
0.028 0.025 1.307 -11.932;
0.000 0.000 0.000 1.000;
----------------------------------------------------
Reading source surface
/nobackup/etsch2/kids/prepost-61kids//81kids_template/surf/rh.white
Done reading source surface
Reading annotation
/nobackup/etsch2/kids/prepost-61kids//81kids_template/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Computing metric properties
Loading source values
number of voxels in search space = 89846
Done loading source values (nvtxs = 98497)
overall max = 4.40787 at vertex 16931
overall min = -3.53455 at vertex 89551
surface nvertices 98497
surface area 67948.492188
surface area 67948.421875
Computing voxel-wise significance
CSDpvalMaxSigMap(): found 214/98497 above 0
NOT Adjusting threshold for 1-tailed test
Searching for Clusters ...
thmin=3.000000 (3.000000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000
Found 5 clusters
Max cluster size 112.311874
Pruning by CW P-Value 0.05
Saving thresholded output to
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.masked.mgh
Saving cluster numbers to
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
Saving cluster pval
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
Constructing output annotation
Writing annotation
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.annot
mri_segstats --seg
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
--exclude 0 --i
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//y.mgh
--avgwf
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.y.ocn.dat
--sum /tmp/mri_glmfit-sim.junk.658856
$Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $
cwd
cmdline mri_segstats --seg
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
--exclude 0 --i
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//y.mgh
--avgwf
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.y.ocn.dat
--sum /tmp/mri_glmfit-sim.junk.658856
sysname Linux
hostname etsch
machine x86_64
user ckuehn
UseRobust 0
Loading
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
Loading
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//y.mgh
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 2 segmentations
Computing statistics for each segmentation
1 1 153 153.000
Reporting on 1 segmentations
Computing spatial average of each frame
0
Writing to
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.y.ocn.dat
mri_segstats done
mri_convert
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
--frame 0
mri_convert
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
--frame 0
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
keeping frame 0
writing to
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh...
Tue Feb 21 17:52:29 CET 2017
Tue Feb 21 17:52:35 CET 2017
mri_glmfit-sim done
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