Freesurfer

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30132 discussions

Re: [Freesurfer] Problem in final analysis
by Douglas N Greve 21 Oct '13

21 Oct '13

fsaverage is already part of the distribution. I don't understand from your email what the problem is. doug On 10/21/2013 10:03 AM, carina(a)van-vlodrop.de wrote: > > Hi Doug, > > > I have already run: > > > recon-all -s subject -qcache -target avgsubject for each subject > > > Is it the same file? > > I am not sure if the brain is really created or if there is a problem > in uploading the brain in qdec. > > Is it possible to get the fsaverage brain from freesurfer to check the > cause of the problem? > > > Thank you > > Carina > > > > > >> ----- Ursprüngliche Nachricht ----- >> Von: Douglas Greve >> Gesendet: 28.09.13 17:46 Uhr >> An: freesurfer(a)nmr.mgh.harvard.edu >> Betreff: Re: [Freesurfer] Problem in final analysis >> >> Hi Carina, run >> >> recon-all -s subject -qcache >> >> for each subject and this will create the file >> >> doug >> >> >> >> >> >> On 9/28/13 5:37 AM, carina(a)van-vlodrop.de wrote: >> >> Dear freesurfer community, we are conducting cortical-thickness >> analysis using freesurfer-4.4.0 and have been experiencing some >> problems with the final analysis steps. We are using the qdec. >> Uploading of the data table has been successful. When we try to >> use the “Analyze” command (design) in the qdec, we get the >> following error message: Error in Analyze: Couldn’t open file >> /data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thickness.fwhm10.fsaverage.mgh >> Obviously, the file was never created during preprocessing. We >> wonder, how to create dir/lh.thickness.fwhm10.fsaverage.mgh and >> would be very grateful for your comments. Yours sincerely, Carina >> $ bugr FREESURFER_HOME: /apps/prod/i486/freesurfer-4.4.0 Build >> stamp: freesurfer-Linux-centos4-stable-pub-v4.4.0 Debian version: >> 5.0.6 Kernel info: Linux 2.6.27.39- 1 –ql-beowulf i686 $ which >> surfer -> /apps/prod/i486/freesurfer-4.4.0/bin/freesurfer Used >> command: qdec/design/Analyze Error message: Error in Analyze: >> Couldn’t open file >> /data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thikness.fwhm10.fsaverage.mgh >> >> >> >> _______________________________________________ Freesurfer >> mailing list Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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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Tcsh-error with Freesurfer
by Philippe Blaes 21 Oct '13

21 Oct '13

Dear Sir / madam, I'm a last year student of Medical Imaging (from Hoge school Universiteit Brussel, HUB). In January i'm defending my thesis. My subject is MRI and Alzheimer's disease. With volumetry I want to show that the Hippocampi have a smaller volume then normal patients. I used the program: SPM, VBM and IBASPM previous year, but I got weird results from those software. My supervisors said that it's probably the best to use a new software, so i'm trying to use Freesurfer. I'm not used to programming with Linux (Xbuntu), so it's a bit difficult for me personally. Also the physicist (who i colaborate with) isn't used to programming. This is my problem: When i open Virtualbox (installed with freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full) I go to file-system -> usr -> local -> freesurfer -> subjects (the map where also the subject"Bert" is in it). In the subject-folder is paste a folder with only T1-Dicom images. After i copied & pasted the DICOM-files in the subjects folder, i go to the "terminal". There I type: "tcsh" to setup freesurfer (I read it on the Freesurfer wiki site). After that I type: recon-all -s <new folder where the new made files are putted in> \ -i $SUBJECTS_DIR/<name of the folder where my DICOM-files are in (here i made an archive of the DICOM-files, extented with .mgz) > \ -autorecon1 When i hit Enter, i get a message that says: "tcsh v6.17.06 has an exit code bug! Please update tcsh!" There is also a new folder created, with some subfolders (BEM, label, scripts , MRI ,etc.). But there is nothing to see in those folders. My question is how can I update tcsh so I can do the recon-all procedure? Hopefully you can help me, Thank you in advance, Kind regards, Philippe Blaes (3rd year Medical Imaging)

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Maybe wrong registration
by Vicente Cutanda 21 Oct '13

21 Oct '13

Hello to everybody, I made a script to extract some structures from a T1 image. The code extract precentral and paracentral gyrus, putamen, nucleus caudate and accumbens. First of all convert from annotation to label, after that I used tkregister (maybe this can be the focus of the problem) to get the coordenates of my T1, finally extract areas with mri_label2vol, mri_convert and fslmaths. I paste the script below: mri_annotation2label --subject ${suje} --hemi lh --outdir $FREESURFER_HOME/subjects/${suje}/annot_labels/ mri_annotation2label --subject ${suje} --hemi rh --outdir $FREESURFER_HOME/subjects/${suje}/annot_labels/ #despues tenemos q calcular la matriz para pasar de freesurfer a espacio .nii tkregister2 --mov ${pathT1}${t1} --noedit --s ${suje} --regheader --reg ${path}register.dat cd ${path} #extraemos aqui precentral i paracentral mri_label2vol --label $FREESURFER_HOME/subjects/${suje}/annot_labels/lh.precentral.label --reg ${path}register.dat --temp ${pathT1}${t1} --subject ${suje} --hemi lh --o l_precent.nii --proj frac 0 1 .1 --fillthresh 0 mri_label2vol --label $FREESURFER_HOME/subjects/${suje}/annot_labels/rh.precentral.label --reg ${path}register.dat --temp ${pathT1}${t1} --subject ${suje} --hemi rh --o r_precent.nii --proj frac 0 1 .1 --fillthresh 0 mri_label2vol --label $FREESURFER_HOME/subjects/${suje}/annot_labels/lh.paracentral.label --reg ${path}register.dat --temp ${pathT1}${t1} --subject ${suje} --hemi lh --o l_paracent.nii --proj frac 0 1 .1 --fillthresh 0 mri_label2vol --label $FREESURFER_HOME/subjects/${suje}/annot_labels/rh.paracentral.label --reg ${path}register.dat --temp ${pathT1}${t1} --subject ${suje} --hemi rh --o r_paracent.nii --proj frac 0 1 .1 --fillthresh 0 mri_convert -rl $FREESURFER_HOME/subjects/${suje}/mri/rawavg.mgz -rt nearest $FREESURFER_HOME/subjects/${suje}/mri/aseg.mgz ${path}aseg.nii #we need to know the codes, caudate is 11 y 50; fslmaths aseg.nii -uthr 11 -thr 11 l_caud.nii fslmaths aseg.nii -uthr 50 -thr 50 r_caud.nii Thanks Vic

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Accuracy
by Vicente Cutanda 21 Oct '13

21 Oct '13

Hello, After run the recon-all instruction, I wanted to extract the paracentral and precentral gyrus in a accurate way. Does anyone knows how can I get extract these areas? Thank you Vicente

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is there a flag for updating recon-all output from 5.0 to 5.3?
by Ruth Carper 18 Oct '13

18 Oct '13

I have about 100 subjects that have been run on 5.0 and I'd like to update them to 5.3. Is there a flag for recon-all that just runs the steps that would be affected by the version change? I seem to recall seeing a flag on the wiki but can't find it now. Maybe it was just for small patches? Thanks.

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Re: [Freesurfer] medial wall crossing the surface
by silver47＠gmx.com 18 Oct '13

18 Oct '13

Not always, but yes, in some instances the aseg crosses. > ----- Original Message ----- > From: Bruce Fischl > Sent: 10/18/13 01:22 PM > To: silver47(a)gmx.com > Subject: Re: [Freesurfer] medial wall crossing the surface > > Does the aseg cross as well? > > > > On Oct 17, 2013, at 10:07 PM, "silver47(a)gmx.com" <silver47(a)gmx.com> wrote: > > > Dear All, > > > > I too am seeing the medial pial surfaces crossing hemispheres in some subjects. > > > > The approach that appears to be working for me involves making copies of brainmask.mgz and aseg.mgz > > For the left hemisphere crossing into the right, edit brainmask.mgz and aseg.mgz to delete voxels at the crossing belonging to the right hemisphere. > > I then run recon-all -autorecon-pial -hemi lh -subjid subject > > followed by returning the brainmask.mgz and aseg.mgz back to their original copy. > > > > This is similarly repeated for the right hemisphere crossing into the left. > > > > Are there any issues or concerns with this approach particularly in regard to thickness or the segmentations? > > > > Thanks, > > > > Paul > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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.

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Comparison between fsaverage and a template created from scratch
by Sophie Maingault 18 Oct '13

18 Oct '13

Hello Experts, I did the procedure to create a template from scratch by following the steps explaining in this page : http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates The objective was to create a template to use it in the command recon-all qcache target my template. So, after creating mytemp2.tif I did mris_register for the subjects used for the template (80 subjects) and then I used make_average_subject --subjects <80 subjects> --out mytemplate. Finally I ran recon-all -qcache target mytemplate in order to visualize my analyzes in QDEC. This procedure seems correct to you because when I just visually compared your template (fsaverage) with mine it looks like very different, as if mine was more smoothed (cf ppt file) ? What do you think ? Best regards. Sophie Maingault

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FS-FAST between-conditions analysis
by Susan Ruiz 18 Oct '13

18 Oct '13

Hi all, When running a functional analysis and comparing two experimental conditions, we observed that there are some voxels/vertices where both condition A and condition B have a positive % signal change from baseline, and condition A has greater activity than condition B. In other regions, both condition A and condition B have negative % signal change from baseline, but condition B has a greater absolute value % signal change (thus relative to baseline condition B has more "deactivation"--a term I am using since you all know what I mean even if the term itself is imperfect). Since, in both cases, the % signal change is technically condition A > condition B, the between-conditions maps do not distinguish these two scenarios. FS-FAST sees these as being the same. Is there a way to tell FS-FAST to cluster these scenarios separately? Is there a compelling reason why I should not consider these different situations? It seems to me that the interpretation of what's taking place in these two scenarios is not identical. Agree or disagree? Can FS-FAST distinguish these with a flag I don't know about? Thank you, ~Sue -- * * ** *** ***** ******** ************* Susan Mosher Ruiz, Ph.D. Research Scientist Boston University School of Medicine Laboratory of Neuropsychology VA Boston Healthcare System smosher(a)bu.edu * * ** *** ***** ******** *************

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medial wall crossing the surface
by silver47＠gmx.com 17 Oct '13

17 Oct '13

Dear All, I too am seeing the medial pial surfaces crossing hemispheres in some subjects. The approach that appears to be working for me involves making copies of brainmask.mgz and aseg.mgz For the left hemisphere crossing into the right, edit brainmask.mgz and aseg.mgz to delete voxels at the crossing belonging to the right hemisphere. I then run recon-all -autorecon-pial -hemi lh -subjid subject followed by returning the brainmask.mgz and aseg.mgz back to their original copy. This is similarly repeated for the right hemisphere crossing into the left. Are there any issues or concerns with this approach particularly in regard to thickness or the segmentations? Thanks, Paul

2 1

aparcstats2table error
by Corinna Bauer 17 Oct '13

17 Oct '13

Hi; I want to put cortical thickness in a table format and am getting an error. command: aparcstats2table --subjectsfile symmetry_subjects.txt --hemi lh --meas thickness --tablefile symm_aparc_stats_rh.txt error: ERROR: The stats file /media/working_tb_drive/symmetry/MMT_08292013/stats/lh.aparc.stats is not found or is too small to be a valid statsfile The statsfile is there and is not empty. Subject names are all in this format ABC_12345678 Any suggestions? Thanks Corinna

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