Re: [Freesurfer] Unpacking mosaic dicoms
Thanks Doug,I downloaded and rerun and changed the permissions but it still says: /Applications/freesurfer/bin/mri_probedicom: Permission denied.Any idea?Thanks,EIraqn On Monday, August 10, 2015 6:18 PM, Douglas N Greve wrote: Hi Eiran, can you download the following two binaries and rerun? First make a backup copy of the ones that are there. Then copy the two below into $FREESURFER_HOME/bin (remove the .mac). ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.mac ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_probedicom.mac On 08/10/2015 08:31 AM, Eiran Vadim Harel wrote: > Hello Freesurfers, > I am using freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0. > I tried unpacking mosaic functional dicoms taken with siemens prisma > scanner using: > > dcmunpack -src > /users/eiran/Desktop/BSMT/201_/Study20150415_184518_65000 -targ > /Applications/freesurfer/BSMT_PROJECT/bsmt201 -run 11 bold nii f.nii > -run 13 bold nii f.nii -run 14 bold nii f.nii -run 15 bold nii f.nii > -run 16 bold nii f.nii -run 17 bold nii f.nii -run 18 bold nii f.nii > -run 19 bold nii f.nii > > I get the following error message: > > > WARNING: file > /users/eiran/Desktop/BSMT/BSMT/201_JACOBY_TAMMY/Study20150415_184518_65000/20TA_Se11_fMRI_Open_Eyes/MR011001001.dcm > > does not contain a Siemens ASCII header > has this file been anonymized? > ERROR: cannot unpack mosiacs without ASCII header > > The files were not anonymized nor changed. > Any ideas how to deal with it? > > Thanks, > Eiran > > > ___ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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.
[Freesurfer] Unpacking mosaic dicoms
Hello Freesurfers,I am using freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.I tried unpacking mosaic functional dicoms taken with siemens prisma scanner using: dcmunpack -src /users/eiran/Desktop/BSMT/201_/Study20150415_184518_65000 -targ /Applications/freesurfer/BSMT_PROJECT/bsmt201 -run 11 bold nii f.nii -run 13 bold nii f.nii -run 14 bold nii f.nii -run 15 bold nii f.nii -run 16 bold nii f.nii -run 17 bold nii f.nii -run 18 bold nii f.nii -run 19 bold nii f.nii I get the following error message: WARNING: file /users/eiran/Desktop/BSMT/BSMT/201_JACOBY_TAMMY/Study20150415_184518_65000/20TA_Se11_fMRI_Open_Eyes/MR011001001.dcm does not contain a Siemens ASCII headerhas this file been anonymized?ERROR: cannot unpack mosiacs without ASCII header The files were not anonymized nor changed.Any ideas how to deal with it? Thanks,Eiran___ 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.
Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
Doug,It works well now,Many thanks!,Eiran
On Friday, March 6, 2015 9:28 PM, Douglas N Greve
wrote:
sorry, gave you a linux binary. Try this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit.mac
On 03/06/2015 02:25 PM, Eiran Vadim Harel wrote:
> Hi Doug,
> It is giving me this error:
> [Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran%
> mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir
> group.glm --nii.gz --surface fsaverage lh
> /Applications/freesurfer/bin/mri_glmfit: line 9: syntax error near
> unexpected token `('
> /Applications/freesurfer/bin/mri_glmfit: line 9: `ELF>
> ?@@(?^@8@,)@?88@8@@@ꨍꨍ `.?%
> ?ʍTT@T@DD??P?td?\?\?Q?t/lib64/ld-linux-x86-64.so.2GNUGNU?L?ьUF?6?'
>
> Thanks,
> Eiran
>
>
> On Friday, March 6, 2015 8:26 PM, Douglas N Greve
> wrote:
>
>
>
> There appears to be a bug in the computation of the fwhm and it appears
> that I fixed the bug somewhere between 5.3 and now. I've put a new
> version of mri_glmfit here
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit
>
> see if that works for you
> doug
>
>
> On 03/06/2015 12:38 PM, Douglas N Greve wrote:
> > Can you upload the ces.nii.gz and cesvar.nii.gz files to our filedrop?f
> >
> > On 03/06/2015 12:23 PM, Eiran Vadim Harel wrote:
> >> Hi Doug,
> >> It seems ok, no isolated voxels.
> >> I attach it.
> >> Any other ideas?
> >> Thanks,
> >> Eiran
> >>
> >>
> >>
> >> On Friday, March 6, 2015 6:22 PM, Douglas N Greve
> >> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >>
> >>
> >>
> >> For some reason the spatial fwhm calculation is failing. This sometimes
> >> happens if the mask is highly fractured. Can you look at
> >> group.glm/mask.nii.gz and see if there are a bunch of isolated voxels?
> >>
> >> On 03/05/2015 11:50 PM, Eiran Vadim Harel wrote:
> >>>
> >>>
> >>>
> >>> Hi Doug,
> >>> Thanks for your reply.
> >>> This is the terminal output:
> >>>
> >>> [Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran%
> >>> mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir
> >>> group.glm --nii.gz --surface fsaverage lh
> >>> Reading source surface
> >>> /Applications/freesurfer/subjects/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
> >>>
> >>
> /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr
> >>> cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir
> >>> group.glm --nii.gz --surface fsaverage lh
> >>> sysname Darwin
> >>> hostname Eran-Harels-MacBook-Pro.local
> >>> machine i386
> >>> user eiran
> >>> FixVertexAreaFlag = 1
> >>> UseMaskWithSmoothing 1
> >>> OneSampleGroupMean 1
> >>> y
> >>>
> >>
> /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz
> >>> logyflag 0
> >>> usedti 0
> >>> labelmask
> >>> /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label
> >>> maskinv 0
> >>> glmdir group.glm
> >>> IllCondOK 0
> >>> ReScaleX 1
> >>> DoFFx 0
> >>> wFile cesvar.nii.gz
> >>> weightinv 1
> >>> weightsqrt 1
> >>> Creating output directory group.glm
> >>> Loading y from
> >>>
> >>
> /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz
> >>> Saving design matrix to group.glm/Xg.dat
> >>> Normalized matrix condition is 1
> >>> Matrix condition is 1
> >>> Found 149955 points in label.
> >>> Pruning voxels by thr: 0.00
> >>> Found 75351 voxels in mask
> >>> Saving mask to group.glm/mask.nii.gz
> >>> Reshaping mriglm->mask...
> >>> search space = 36561.555889
> >>> DOF = 26
> >>> Starting fit and test
> >>> Fit completed in 0.0542833 minutes
> >>> C
Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
Hi Doug,It is giving me this
error:[Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran%
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm
--nii.gz --surface fsaverage lh/Applications/freesurfer/bin/mri_glmfit: line 9:
syntax error near unexpected token `('/Applications/freesurfer/bin/mri_glmfit:
line 9: `ELF> ?@@(?^@8 @,)@?88@8@@@ꨍꨍ `.?%
?ʍTT@T@DD??P?td?\?\?Q?t/lib64/ld-linux-x86-64.so.2GNUGNU?L?ьUF?6?'
Thanks,Eiran
On Friday, March 6, 2015 8:26 PM, Douglas N Greve
wrote:
There appears to be a bug in the computation of the fwhm and it appears
that I fixed the bug somewhere between 5.3 and now. I've put a new
version of mri_glmfit here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit
see if that works for you
doug
On 03/06/2015 12:38 PM, Douglas N Greve wrote:
> Can you upload the ces.nii.gz and cesvar.nii.gz files to our filedrop?f
>
> On 03/06/2015 12:23 PM, Eiran Vadim Harel wrote:
>> Hi Doug,
>> It seems ok, no isolated voxels.
>> I attach it.
>> Any other ideas?
>> Thanks,
>> Eiran
>>
>>
>>
>> On Friday, March 6, 2015 6:22 PM, Douglas N Greve
>> wrote:
>>
>>
>>
>> For some reason the spatial fwhm calculation is failing. This sometimes
>> happens if the mask is highly fractured. Can you look at
>> group.glm/mask.nii.gz and see if there are a bunch of isolated voxels?
>>
>> On 03/05/2015 11:50 PM, Eiran Vadim Harel wrote:
>>>
>>>
>>>
>>> Hi Doug,
>>> Thanks for your reply.
>>> This is the terminal output:
>>>
>>> [Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran%
>>> mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir
>>> group.glm --nii.gz --surface fsaverage lh
>>> Reading source surface
>>> /Applications/freesurfer/subjects/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
>>>
>> /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr
>>> cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir
>>> group.glm --nii.gz --surface fsaverage lh
>>> sysname Darwin
>>> hostname Eran-Harels-MacBook-Pro.local
>>> machine i386
>>> user eiran
>>> FixVertexAreaFlag = 1
>>> UseMaskWithSmoothing 1
>>> OneSampleGroupMean 1
>>> y
>>>
>> /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz
>>> logyflag 0
>>> usedti 0
>>> labelmask
>>> /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label
>>> maskinv 0
>>> glmdir group.glm
>>> IllCondOK 0
>>> ReScaleX 1
>>> DoFFx 0
>>> wFile cesvar.nii.gz
>>> weightinv 1
>>> weightsqrt 1
>>> Creating output directory group.glm
>>> Loading y from
>>>
>> /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz
>>> Saving design matrix to group.glm/Xg.dat
>>> Normalized matrix condition is 1
>>> Matrix condition is 1
>>> Found 149955 points in label.
>>> Pruning voxels by thr: 0.00
>>> Found 75351 voxels in mask
>>> Saving mask to group.glm/mask.nii.gz
>>> Reshaping mriglm->mask...
>>> search space = 36561.555889
>>> DOF = 26
>>> Starting fit and test
>>> Fit completed in 0.0542833 minutes
>>> Computing spatial AR1 on surface
>>> Residual: ar1mn=inf, ar1std=nan, gstd=nan, fwhm=nan
>>> Writing results
>>> osgm
>>> maxvox sig=5.1359 F=31.1425 at index 47512 0 0 seed=1425981217
>>> mri_glmfit done
>>>
>>> Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran%
>>> mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166
>>> cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm
>>> --glmdir group.glm --nii.gz --surface fsaverage lh
>>> SURFACE: fsaverage lh
>>> log file is group.glm/cache.mri_glmfit-sim.log
>>>
>>> cd
>>>
>> /applications/freesurfer/bsmt_project/doors_group_51014/doors11.lh/r-vs-nr
>>> /Applications/freesurfer/bin/mri_glmfit-sim
>>> --glmdir group.glm --cache 3 pos --cwpvalthresh .0166
>>
Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
Hi Doug,It seems ok, no isolated voxels.I attach it.Any other ideas?Thanks,Eiran On Friday, March 6, 2015 6:22 PM, Douglas N Greve wrote: For some reason the spatial fwhm calculation is failing. This sometimes happens if the mask is highly fractured. Can you look at group.glm/mask.nii.gz and see if there are a bunch of isolated voxels? On 03/05/2015 11:50 PM, Eiran Vadim Harel wrote: > > > > > Hi Doug, > Thanks for your reply. > This is the terminal output: > > [Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% > mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir > group.glm --nii.gz --surface fsaverage lh > Reading source surface > /Applications/freesurfer/subjects/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 > /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr > cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir > group.glm --nii.gz --surface fsaverage lh > sysname Darwin > hostname Eran-Harels-MacBook-Pro.local > machine i386 > user eiran > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > OneSampleGroupMean 1 > y > >/Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz > logyflag 0 > usedti 0 > labelmask > /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label > maskinv 0 > glmdir group.glm > IllCondOK 0 > ReScaleX 1 > DoFFx 0 > wFile cesvar.nii.gz > weightinv 1 > weightsqrt 1 > Creating output directory group.glm > Loading y from > /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz > Saving design matrix to group.glm/Xg.dat > Normalized matrix condition is 1 > Matrix condition is 1 > Found 149955 points in label. > Pruning voxels by thr: 0.00 > Found 75351 voxels in mask > Saving mask to group.glm/mask.nii.gz > Reshaping mriglm->mask... > search space = 36561.555889 > DOF = 26 > Starting fit and test > Fit completed in 0.0542833 minutes > Computing spatial AR1 on surface > Residual: ar1mn=inf, ar1std=nan, gstd=nan, fwhm=nan > Writing results > osgm > maxvox sig=5.1359 F=31.1425 at index 47512 0 0 seed=1425981217 > mri_glmfit done > > Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% > mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 > cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm > --glmdir group.glm --nii.gz --surface fsaverage lh > SURFACE: fsaverage lh > log file is group.glm/cache.mri_glmfit-sim.log > > cd > /applications/freesurfer/bsmt_project/doors_group_51014/doors11.lh/r-vs-nr > /Applications/freesurfer/bin/mri_glmfit-sim > --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 > > $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ > Wed Mar 4 20:55:33 IST 2015 > Darwin Eran-Harels-MacBook-Pro.local 10.8.0 Darwin Kernel Version > 10.8.0: Tue Jun 7 16:33:36 PDT 2011; > root:xnu-1504.15.3~1/RELEASE_I386 i386 > eiran > setenv SUBJECTS_DIR /Applications/freesurfer/subjects > FREESURFER_HOME /Applications/freesurfer > > Original mri_glmfit command line: > cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir > group.glm --nii.gz --surface fsaverage lh > > DoSim = 0 > UseCache = 1 > DoPoll = 0 > DoPBSubmit = 0 > DoBackground = 0 > DiagCluster = 0 > gd2mtx = dods > fwhm = nan > ERROR: cannot find > /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd > > Any ideas? > Thanks, > Eiran > > Subject: Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638 > Date: Mon, 02 Mar 2015 14:17:39 -0500 > From: Douglas N Greve <mailto:gr...@nmr.mgh.harvard.edu>> > Reply-To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu>> > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > That is strange. Can you send the full terminal output from the first > call to mri_glmfit-sim? > doug > > On 02/23/2015 03:49 AM, Eiran Vadim Harel wrote: > > > Hello Freesurfers, > > > > I use freesurfer v5.3.0 > > > > When I do group analysis correction for multiple comparisons for lh as > > follows: > > > > mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir > > group.glm --nii.gz --surface fsaverage lh > > > > mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166
Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
Hi Doug,Thanks for your reply.This is the terminal output: [Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lhReading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.whiteNumber of vertices 163842Number of faces 327680Total area 65416.648438AvgVtxArea 0.399267AvgVtxDist 0.721953StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $cwd /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nrcmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh sysname Darwinhostname Eran-Harels-MacBook-Pro.localmachine i386user eiranFixVertexAreaFlag = 1UseMaskWithSmoothing 1OneSampleGroupMean 1y /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gzlogyflag 0usedti 0labelmask /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.labelmaskinv 0glmdir group.glmIllCondOK 0ReScaleX 1DoFFx 0wFile cesvar.nii.gzweightinv 1weightsqrt 1Creating output directory group.glmLoading y from /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gzSaving design matrix to group.glm/Xg.datNormalized matrix condition is 1Matrix condition is 1Found 149955 points in label.Pruning voxels by thr: 0.00Found 75351 voxels in maskSaving mask to group.glm/mask.nii.gzReshaping mriglm->mask...search space = 36561.555889DOF = 26Starting fit and testFit completed in 0.0542833 minutesComputing spatial AR1 on surfaceResidual: ar1mn=inf, ar1std=nan, gstd=nan, fwhm=nanWriting results osgm maxvox sig=5.1359 F=31.1425 at index 47512 0 0 seed=1425981217mri_glmfit done Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lhSURFACE: fsaverage lhlog file is group.glm/cache.mri_glmfit-sim.log cd /applications/freesurfer/bsmt_project/doors_group_51014/doors11.lh/r-vs-nr/Applications/freesurfer/bin/mri_glmfit-sim--glmdir group.glm --cache 3 pos --cwpvalthresh .0166 $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $Wed Mar 4 20:55:33 IST 2015Darwin Eran-Harels-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386eiransetenv SUBJECTS_DIR /Applications/freesurfer/subjectsFREESURFER_HOME /Applications/freesurfer Original mri_glmfit command line:cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh DoSim = 0UseCache = 1DoPoll = 0DoPBSubmit = 0DoBackground = 0DiagCluster = 0gd2mtx = dodsfwhm = nanERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd Any ideas?Thanks,Eiran Subject: Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638 Date: Mon, 02 Mar 2015 14:17:39 -0500 From: Douglas N Greve Reply-To: Freesurfer support list To: freesurfer@nmr.mgh.harvard.edu That is strange. Can you send the full terminal output from the first call to mri_glmfit-sim? doug On 02/23/2015 03:49 AM, Eiran Vadim Harel wrote: > Hello Freesurfers, > > I use freesurfer v5.3.0 > > When I do group analysis correction for multiple comparisons for lh as > follows: > > mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir > group.glm --nii.gz --surface fsaverage lh > > mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 > > I get this error message: > > ERROR: cannot find > /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd > > For the mkanalysis-sess i used fwhm = 5. > > When i do the same for mni305 and use: > > mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir > group.glm --nii.gz > > mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166 > > It works well without an error. > > Thanks, > Eiran ___ 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.
[Freesurfer] mri_glmfit-sim Error
Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 I get this error message: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd For the mkanalysis-sess i used fwhm = 5. When i do the same for mni305 and use: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166 It works well without an error. Thanks,Eiran___ 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.
Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 I get this error message: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd For the mkanalysis-sess i used fwhm = 5. When i do the same for mni305 and use: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166 It works well without an error. Thanks,Eiran On Monday, February 23, 2015 10:37 AM, "freesurfer-requ...@nmr.mgh.harvard.edu" wrote: Mailing list subscription confirmation notice for mailing list Freesurfer We have received a request from 79.177.55.71 for subscription of your email address, "eiranha...@yahoo.com", to the freesurfer@nmr.mgh.harvard.edu mailing list. To confirm that you want to be added to this mailing list, simply reply to this message, keeping the Subject: header intact. Or visit this web page: https://mail.nmr.mgh.harvard.edu/mailman/confirm/freesurfer/5db71d8d19a634948b059d302f95d798f665a638 Or include the following line -- and only the following line -- in a message to freesurfer-requ...@nmr.mgh.harvard.edu: confirm 5db71d8d19a634948b059d302f95d798f665a638 Note that simply sending a `reply' to this message should work from most mail readers, since that usually leaves the Subject: line in the right form (additional "Re:" text in the Subject: is okay). If you do not wish to be subscribed to this list, please simply disregard this message. If you think you are being maliciously subscribed to the list, or have any other questions, send them to freesurfer-ow...@nmr.mgh.harvard.edu. 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 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.
Re: [Freesurfer] recon-all problem
It still does not find the file. [shimshon:TrioTim-35101-20120912-135155-195000] (nmr-stable5.0-env) recon-all -i ./cluster/archive/301/siemens/TrioTim-35101-20120912-135155-195000/MR.1.3.12.2.1107.5.2.32.35101.3.2012091214284986179598358 -i ./cluster/archive/301/siemens/TrioTim-35101-20120912-135155-195000/MR.1.3.12.2.1107.5.2.32.35101.3.2012091214340478463998836 -s 39_bay6 ERROR: cannot find ./cluster/archive/301/siemens/TrioTim-35101-20120912-135155-195000/MR.1.3.12.2.1107.5.2.32.35101.3.2012091214284986179598358 Linux shimshon 2.6.18-308.13.1.el5 #1 SMP Tue Aug 21 17:10:18 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Fri Sep 14 13:32:22 EDT 2012 > > /cluster/archive/301/siemens/TrioTim-35101-20120912-135155-195000/MR.1.3.12.2.1107.5.2.32.35101.3.2012091214284986179598358 > > > > On 09/14/2012 01:01 PM, Eiran Vadim Harel wrote: >> Hi, >> >> 3 T1_MPRAGE_sag_short 3.39 2430 7 unknown ROW 190 >> /cluster/archive/301/siemens/TrioTim-35101-20120912-135155-195000/MR.1.3.12.2.1107.5.2.32.35101.3.2012091214284986179598358 >> >> >> This is what it gives me when i do dcmunpack. What shall i use as the >> file >> indicator in the recon-all -i ./ >> Thanks! >> eiran >> >> >> >> >>> You'll need to run dcmunpack without the -martinos flag. This will >>> (eventually) give you a list of runs and corresponding file names. Find >>> the one that is the MPRAGE you want to recon, and pass that as -i to >>> recon-all. Unfortunately the name change makes it harder/slower to >>> unpack data here. >>> doug >>> >>> On 09/14/2012 11:06 AM, Eiran Vadim Harel wrote: >>>> Hi all, >>>> Is there a change in the unpacking of the MPRAGE and DICOM files? >>>> The names of the files have changed. >>>> what file name should be put in the command: >>>> recon-all -i./file name -s subjectname >>>> Thanks, >>>> Eiran >>>> ___ >>>> 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 >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> ___ >>> 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 > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > ___ 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.
Re: [Freesurfer] recon-all problem
Hi, 3 T1_MPRAGE_sag_short 3.39 2430 7 unknown ROW 190 /cluster/archive/301/siemens/TrioTim-35101-20120912-135155-195000/MR.1.3.12.2.1107.5.2.32.35101.3.2012091214284986179598358 This is what it gives me when i do dcmunpack. What shall i use as the file indicator in the recon-all -i ./ Thanks! eiran > You'll need to run dcmunpack without the -martinos flag. This will > (eventually) give you a list of runs and corresponding file names. Find > the one that is the MPRAGE you want to recon, and pass that as -i to > recon-all. Unfortunately the name change makes it harder/slower to > unpack data here. > doug > > On 09/14/2012 11:06 AM, Eiran Vadim Harel wrote: >> Hi all, >> Is there a change in the unpacking of the MPRAGE and DICOM files? >> The names of the files have changed. >> what file name should be put in the command: >> recon-all -i./file name -s subjectname >> Thanks, >> Eiran >> ___ >> 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 > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > ___ > 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.
[Freesurfer] recon-all problem
Hi all, Is there a change in the unpacking of the MPRAGE and DICOM files? The names of the files have changed. what file name should be put in the command: recon-all -i./file name -s subjectname Thanks, Eiran ___ 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.
[Freesurfer] Error in preprocessing
Hi, I am using stable5.0-env. I have run the pre[processing command: preproc-sess -s 1411_MC -surface fsaverage lhrh -mni305 -fwhm 5 -per-run I got this ERROR message: /autofs/space/shimshon_002/users/eiran/contproc/1411_MC RunList: 005 006 007 --- ** --- --- Motion Correcting Run 005 --- --- ** --- sess = 1411_MC Fri Aug 5 11:51:17 EDT 2011 mc-afni2 --i 005/f.nii --t 005/template.nii --o 005/fmcpr.nii --mcdat 005/fmcpr.mcdat ERROR: cannot find AFNI command 3dvolreg My PROJECT DIR: /space/shimshon/2/users/eiran/contproc SUBJECTS_DIR: /space/shimshon/2/users/eiran/subjects Is there a way to solve it? Thanks, Eiran ___ 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.
[Freesurfer] funcroi-config -frame question
Hello, I did an FIR analysis and want to get the activation measure for specific ROI at consequent time frames. mkanalysis-sess -analysis context_FIR.rh -surface fsaverage rh -fwhm 5 -paradigm sca_wca.par -event-related -fir 4.4 17.6 -refeventdur 2.2 -mcextreg -TR 2.2 -nconditions 2 -force mkcontrast-sess -analysis context_FIR.rh -contrast strongweak-vs-fix -a 1 -a 2 -c 0 selxavg3-sess -s 0121_MC -analysis context_FIR.rh -force I then gave separate funcroi-config commands to each time frame 0-7 funcroi-config -roi v1.rh.frame0 -label rh.V1 -analysis context_FIR.rh -frame 0 -force funcroi-table-sess -o v1.rh.frame0.table.txt -roi v1.rh.frame0 -a context_FIR.rh -s 0121_MC -map cespct it created the text file with: 0121_MC 84.034 when i ran it for the rest of the time frames it gave me the same number: funcroi-config -roi v1.rh.frame7 -label rh.V1 -analysis context_FIR.rh -frame 7 -force funcroi-table-sess -o v1.rh.frame7.table.txt -roi v1.rh.frame7 -a context_FIR.rh -s 0121_MC -map cespct It gave the same output in the text file: 0121_MC 84.034 I am using freesurfer 5 on shimshon: the project directory: /space/shimshon/2/users/eiran/contproc2 SUBJECT_DIR- /space/shimshon/2/users/eiran/subjects I made the frames according to your instructions on a request from dec. 2010 with the same problem: > > Currently, it is not as convenient to do this with version 5. You have > to create a condition-vs-fixation for each condition that you want a > time course for. Then for each condition, you need to run > funcroi-table-sess for each time point (using the -frame option), then > construct the waveforms from these files. It's a bit of a hassle, but > scriptable. Thanks! ___ 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.
