Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] command not found
by Louis Nicholas Vinke 28 May '13

28 May '13

Hi Clelia, That mv command is failing presumably because SetUpFreeSurfer.txt does not exist in that directory. What are you trying to do with the mv command? It does look like freesurfer was sourced successfully. Are the FreeSurfer related commands still not found? Don't forget to cc the freesurfer mailing list. -Louis On Fri, 24 May 2013, clelia pellicano wrote: > Hi Louise, > I'm now using tcsh. Here what I did > > [dyn1097-8:~] cpellica% setenv FREESURFER_HOME /Applications/freesurfer > [dyn1097-8:~] cpellica% source /Applications/freesurfer/SetUpFreesurfer.csh > -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Applications/freesurfer > FSFAST_HOME /Applications/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Applications/freesurfer/subjects > MNI_DIR /Applications/freesurfer/mni > FSL_DIR /usr/local/fsl > [dyn1097-8:~] cpellica% mv SetUpFreeSurfer.txt SetUpFreeSurfer.csh > mv: rename SetUpFreeSurfer.txt to SetUpFreeSurfer.csh: No such file or directory > > Do you have any advice? > > Thanks > > Clelia > > > > > > On Fri, May 24, 2013 at 3:04 PM, Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> wrote: > Hi Clelia, > What do you run to source FS and do you get any output in your terminal after doing so? What operating system are > you running? You might try using c-shell instead of bash. > -Louis > > On Fri, 24 May 2013, clelia pellicano wrote: > > Hi Louis, > thank you for your answer. > I sourced freesurfer again, but I still get 'command not found'. > What can I try? > Thank you, > > Clelia > > > On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> wrote: > Hi Clelia, > If this is in a new terminal then you'll have to source freesurfer again. See here for details: > https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration > -Louis > > On Wed, 22 May 2013, clelia pellicano wrote: > > Hi, > I have run recon-all -s bert -all to try my installation and it worked. > Now, when I try to use other command (and also again recon-all -s bert -all) I always get > this: > > dyn1097-8:subjects cpellica$ tkmedit bert orig.mgz > -bash: tkmedit: command not found > dyn1097-8:subjects cpellica$ tkmedit -s bert orig.mgz > -bash: tkmedit: command not found > dyn1097-8:subjects cpellica$ tksurfer -s bert rh pial > -bash: tksurfer: command not found > dyn1097-8:subjects cpellica$ qdec > -bash: qdec: command not found > dyn1097-8:subjects cpellica$ recon-all help > -bash: recon-all: command not found > dyn1097-8:subjects cpellica$ recon-all -s bert -all > -bash: recon-all: command not found > > > I don't know how to do. Please, could you help me? > > Thanks > > Clelia > > > > > 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. > > > > > >

3 3

mri_anatomical_stats segmentation fault
by Rob Tennyson 28 May '13

28 May '13

Hi All, I'm running "mris_anatomical_stats" with a few manually defined labels. For a few of my subjects, I am getting the error: "Segmentation fault" on one of the labels. However, the other manually defined labels process without any errors on these same subjects. For example, I am running "mri_anatomical_stats" on subject 33_bay6 with a manually defined ERC label, a manually defined PHC label, and a manually defined medial frontal gyrus label. The only label that runs an error for this subject is the PHC label. This PHC label runs without any errors on the rest of my subjects. Here is what is displayed when running a label that fails: "> mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b 33_bay6 lh limiting computations to label lh.PHC_1.label. reading volume /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz... reading input surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... reading input pial surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial... reading input white surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... Segmentation fault" Does anyone know what may be causing the Segmentation fault and what steps I should take to fix it? Thank you for your help! Rob

3 2

nuintensitycor and skullstrip problems
by LAOUCHEDI MAKHLOUF 28 May '13

28 May '13

hi i send you the rawavg.mgz of the subject with the massive artefact. i inform you that i proceeded differently by splitting the recon-all -all into three steps (as in freesurfer wiki) : (1) recon-all -autorecon1, (2) recon-all -autorecon2 (3) recon-all -autorecon3. i just finished with the first step which still didn't work for some subjects so i deleted then in my SUBJECTS_DIR then i run "recon-all -i" to regenerate them. after that i re-run "recon-all -autorecon1" and it worked even for the subject with the artefacted rawavg.mgz i am sending you. i noticed also that some extra cerebral structures like dura is not fully removed after the skullstripping step, and i reviewed some of my previous datasets i processed with freesurfer and i noticed that the cortical ribbon (containing the cortical parcellation) fits well the gray matter. so is a wise idea to not bother a lot about these "some" extra cerebral structures left and just go forward with the rest of the recon-all pipeline (but of course i'll take a look a posteriori). Thanks

2 1

minor bug report
by Joseph Dien 28 May '13

28 May '13

when I run: isxconcat-sess -sf sessidlist.dat -analysis CPA.sm05.lh -all-contrasts -o secondLevel I get the error messages: secondLevel/CPA.sm05.mni305/log/isxconcat.log stat: illegal option -- c usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file ...] stat: illegal option -- c usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file ...] stat: illegal option -- c usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file …] ... I'm assuming this isn't a serious problem as it just seems to affect what goes into the log file but thought you might want to know. This is on OS X 10.8.2 with Freesurfer 5.2.0. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com//

3 3

fix talairach transform
by LAOUCHEDI MAKHLOUF 28 May '13

28 May '13

Hi i have a problem when running "recon-all -all", so i decided to split the process into three staps : "recon-all -autorecon1", ""recon-all -autorecon2" and "recon-all -autorecon3". i have just finished with the first step (recon-all -autorecon1) and looked for misalignment in talairach transform for all subjects using "tkregister2 --mgz --s ctr1 --fstal" (i can't use "--surf orig " because i haven't the surfaces yet). so i used the small red cross in the coronal, sagittal and axial views to align as much as possible. my goal is to extract the cortical labels (cortical parcellation). is it necessary to have a precise talairach transform just for this purpose ? Thank you

2 1

nuintensitycor and skullstrip problems
by LAOUCHEDI MAKHLOUF 28 May '13

28 May '13

hi i send you further information of the -nuintensitycor and skullstrip problem,about three control subjects. after running "recon_all -i", i decided to process my data step by step, i run "recon_all -autorecon1" for all of them and it ended with errors. i picked up three cases of the recon-all.log file : subject 1: #@# Nu Intensity Correction Mon May 27 18:08:32 CEST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home_cluster/mlaouche/freesurf_makh/ctr3/mri /home_cluster/amesse/software/freesurfer5.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon May 27 18:08:36 CEST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.12456 /home_cluster/mlaouche/freesurf_makh/ctr3/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12456/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12456/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=7.05, 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.12456/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon May 27 18:23:46 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.12456/nu0.mnc ./tmp.mri_nu_correct.mni.12456/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12456/0/ ./tmp.mri_nu_correct.mni.12456/ is a directory but not writeable [mlaouche@cn09:/home_cluster/mlaouche/freesurf_makh/ctr3/mri/] [2013-05-27 18:23:56] running: /home_cluster/amesse/software/freesurfer5.1/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.12456/0/ ./tmp.mri_nu_correct.mni.12456/nu0.mnc ./tmp.mri_nu_correct.mni.12456/nu1.imp Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ctr3 exited with ERRORS at Mon May 27 18:47:13 CEST 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting subject 2: #@# Nu Intensity Correction Mon May 27 18:08:21 CEST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home_cluster/mlaouche/freesurf_makh/ctr5/mri /home_cluster/amesse/software/freesurfer5.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon May 27 18:08:31 CEST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.12252 /home_cluster/mlaouche/freesurf_makh/ctr5/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12252/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12252/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=7.07, 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.12252/nu0.mnc... tee: ./mri_nu_correct.mni.log: Input/output error -------------------------------------------------------- Iteration 1 Mon May 27 18:23:44 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.12252/nu0.mnc ./tmp.mri_nu_correct.mni.12252/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12252/0/ ./tmp.mri_nu_correct.mni.12252/ is a directory but not writeable [mlaouche@cn09:/home_cluster/mlaouche/freesurf_makh/ctr5/mri/] [2013-05-27 18:23:56] running: /home_cluster/amesse/software/freesurfer5.1/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.12252/0/ ./tmp.mri_nu_correct.mni.12252/nu0.mnc ./tmp.mri_nu_correct.mni.12252/nu1.imp Computing ranges for each class.: ............................................. Processing:.................................................................Done Fitting splines: .............................................................. Computing ranges for each class.: ............................................. Processing:.................................................................Done Computing ranges for each class.: ............................................. Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ctr5 exited with ERRORS at Mon May 27 19:13:37 CEST 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting subject 3: #@# Nu Intensity Correction Mon May 27 18:08:34 CEST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home_cluster/mlaouche/freesurf_makh/ctr6/mri /home_cluster/amesse/software/freesurfer5.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon May 27 18:08:38 CEST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 mkdir: cannot create directory `./tmp.mri_nu_correct.mni.12552': Input/output error tee: ./mri_nu_correct.mni.log: Input/output error tmpdir is ./tmp.mri_nu_correct.mni.12552 Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

2 1

Re: [Freesurfer] rerun interrupted processes
by Bruce Fischl 28 May '13

28 May '13

Hi Valeria can you address this type of question to the list so that others can answer and learn from the answers? Yes, you can run recon-all -make all -s <subject id> and it should pick up from where it left off Bruce On Tue, 28 May 2013, Valeria Contarino wrote: > Dear Bruce, > I have a new question for you. > I was running 30 subjects when processes were interrupted because of no more space left on device. > Do I have the chance for starting again the processes from where they stopped? > > Thank you. > > Regards, > Valeria > >

1 0

recon-all with FLAIR error no FSL installed
by Popescu, Veronica 28 May '13

28 May '13

Dear all, I am running FreeSurfer 5.3 with FLAIR refinement. I do not have FSL installed. I do get results but there's an error message in the log file (attached) about the FSL installation missing. How bad is it? Do I have to rerun everything with FSL installed? And if so, is there any version that is preferable? Thank you very much in advance! Best wishes, Veronica

3 6

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
by Salil Soman 27 May '13

27 May '13

Dear Doug, Thank you for your email. Following up on our previous discussions: 1) *bbregister fail *- this was happening because of error from fslregister. The variable fsvol was translating to "ERROR". In fslregister th value for fsvol is set to brainmask, along with numerous other parameters being initialized. By adding the line "set fsvol = brain mask" (without quotes) at the beginning of the section "#Convert reference to analyze" the CentOS 6 version I am running on ubuntu 12.04 (with SGE), now works. 2) when you suggested I run bbregister on the lowb.nii file, was it because I had suggested I wanted to register to a 2D ADC map? If I want to instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I want to get value from instead of lowb.nii? I ended up running 3) for the mri_vol2vol step - I had to change targ to fstarg, and I left out the interp flag so it would do its default trilinear: mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat --inv 4) I would like to get the segmentations from aparc+aseg.mgz as the areas where I get the values summed. So I entered mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats but then I received this error: ERROR: dimension mismatch between input volume and seg input 224 224 170 seg 256 256 256 * * *So, in summary, while I've fixed bbregister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.* Any ideas on how to proceed? Thanks, Sal On Sat, May 25, 2013 at 11:51 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu>wrote: > > On 5/25/13 1:39 PM, Salil Soman wrote: > > Thank you Doug. > > Just so I am clear - is the anatomical the nifti T1.mgz or is it a > different file. From your email I gather should do the following: > > *1) Use bbregister to register the lowb image to the anatomical. This > creates a registration matrix.* > > bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat > > That is right, but add --t2 (since it is t2 weighted). > > > *2) Use mri_vol2vol and the registration to map the ADC map to the > anatomical* > > mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg > > Use the ADC as the moveable (not lowb, but use the lowb for > bbregister). The target volume should be the T1.mgz (or any conformed > volume). The output will be the adc in the anatomical space (not sure why > you call it vol2diff). > > *3) use mri_segstats to extract the values* > > *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats > > The input would be the adc volume mapped the anatomical space. I would > use WMParcStatsLUT.txt or else you'll get a billion different areas not > represented in wmparc. You may also want to add "--seg-erode 1" to erode > the segmentations by a voxel. This helps to prevent partial voluming. > > doug > > > > Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. > ADC), $vol2diff is the output image of the registration, and fa.stats will > be my output stats table? > > I suspect there is part of the syntax for these tools I do not > understand. Also, what input would $vol be? > > Best wishes, > > Sal > > > On Sat, May 25, 2013 at 10:06 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu > > wrote: > >> >> Hi Sal, yes you can. Use bbregister to register the lowb image to the >> anatomical. This creates a registration matrix. Use mri_vol2vol and the >> registration to map the ADC map to the anatomical, then use mri_segstats to >> extract the values >> doug >> >> ps. Please post questions to the FS list instead of us directly so that >> others can benefit and it gets archived. thanks! >> >> >> >> On 5/25/13 1:03 PM, Salil Soman wrote: >> >>> Dear Dr. Greve, >>> >>> Is it possible to register a nonstructural MR sequences (e.g. an ADC >>> map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using >>> the segmentation from the aseg (or aparc+aseg) file to output a mean ADC >>> value for each anatomic area segmented? >>> >>> Thank you for your time and consideration. >>> >>> Best wishes, >>> >>> Sal >>> >>> Salil Soman, MD, MS >>> >> >> >> >> 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. >> >> > >

2 6

white matter volume per lobe...
by Gonzalo Rojas Costa 27 May '13

27 May '13

Hi: I used the following commands to get the cortical volume per each lobe: mri_annotation2label --subject OAS1_0001_MR1 --hemi rh --lobesStrict lobulos --seg lobulos --stat lobulos mri_annotation2label --subject OAS1_0001_MR1 --hemi lh --lobesStrict lobulos --seg lobulos --stat lobulos mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_rh -b OAS1_0001_MR1 rh mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_lh -b OAS1_0001_MR1 lh Which commands (sintaxis) must I use to compute the white matter volume per each lobe ?... I tested the mri_aparc2aseg and mri_segstats commans with different options, but I couldn't get the volume that I need... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer