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30132 discussions

Re: [Freesurfer] WM/GM boundary changes and control points
by EK Kim 15 Oct '12

15 Oct '12

I've been struggling to upload the file to the ftp server, but failed in several times. Sorry for bothering you, but I will send an e-mail when the uploading is done. Best, EK 2012/10/14 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > I found EK_test.zip, but neither tar nor unzip knows how to uncomress it. > What format is it? Or maybe it's corrupted... > > > On Sat, 13 Oct 2012, EK Kim wrote: > > Bruce, and other experts, thank you for your time :) >> >> I'm now uploading the data folder (before cp and after cp) to the >> freesurfer incoming directory. >> >> >> We obtained the 3D-SPGR axial images using 3T GE system which have >> 8HRBRAIN receiving coil. >> Data acquisition matrix is 320-by192, FOV is 200-by-200. >> >> Other parameters; >> slice thickness =1.5 >> TR=5.924 >> TE=1.472 >> Flip angle: 20 >> Inversion Time=400 >> Imaging Frequency 127.88 >> Percent Phase FOV =80 >> >> Sincerely, >> >> EK >> >> >> >> 2012/10/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi EK >> >> that is a really low-contrast image. Can you tell me about the >> acquisition parameters and resolution? Also, I can't >> diagnose your problem from just the volume I'll need the entire >> (tarred and gzipped) subject directory. Finally, >> please cc the list on these emails so that others can help you! >> >> Bruce >> On Thu, 11 Oct 2012, EK Kim wrote: >> >> I uploaded the files to transfer/incoming folder. >> >> >> Best, >> >> EK >> >> 2012/10/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> If you upload the subject to our FTP site I will take a >> look >> Bruce >> >> >> >> On Oct 10, 2012, at 9:29 PM, EK Kim <ksea03(a)gmail.com> wrote: >> >> Thank you for your answer. >> I'm not sure I understand your question right, >> but I just processed the file using following procedures. >> 1. recon-all -autorecon1 -nuintensitycor-3T (because mine was >> 3T) >> 2. skullstripping brain mask using gcuts >> 3. adding control points (only on the left hemisphere) >> 4. recon-all -autorecon2-cp >> and this figure was made by a commnad line, [tkmedit wm.mgz >> -aux >> brain.mgz -surfs]. >> Best, >> EK. >> >> 2012/10/10 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> what was the name of the file that you transferred? >> On Wed, 10 Oct 2012, EK Kim wrote: >> >> I already uploaded this problem 2 days >> ago, reprocessing the subject to make >> sure about control points. >> However when I added the control points >> to the left hemisphere, >> the right hemisphere surface was changed >> severely. >> I used the command line, recon-all >> -autorecon2-cp -s subjectID. >> Could you tell me why does it occur and >> how to deal with it? >> >> >> Best, >> >> EK >> >> >> >> >> 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<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(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >> >> >>

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Re: [Freesurfer] WM/GM boundary changes and control points
by EK Kim 13 Oct '12

13 Oct '12

Bruce, and other experts, thank you for your time :) I'm now uploading the data folder (before cp and after cp) to the freesurfer incoming directory. We obtained the 3D-SPGR axial images using 3T GE system which have 8HRBRAIN receiving coil. Data acquisition matrix is 320-by192, FOV is 200-by-200. Other parameters; slice thickness =1.5 TR=5.924 TE=1.472 Flip angle: 20 Inversion Time=400 Imaging Frequency 127.88 Percent Phase FOV =80 Sincerely, EK 2012/10/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi EK > > that is a really low-contrast image. Can you tell me about the acquisition > parameters and resolution? Also, I can't diagnose your problem from just > the volume I'll need the entire (tarred and gzipped) subject directory. > Finally, please cc the list on these emails so that others can help you! > > Bruce > > On Thu, 11 Oct 2012, EK Kim wrote: > > I uploaded the files to transfer/incoming folder. >> >> >> Best, >> >> EK >> >> 2012/10/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> If you upload the subject to our FTP site I will take a look >> Bruce >> >> >> >> On Oct 10, 2012, at 9:29 PM, EK Kim <ksea03(a)gmail.com> wrote: >> >> Thank you for your answer. >> I'm not sure I understand your question right, >> but I just processed the file using following procedures. >> 1. recon-all -autorecon1 -nuintensitycor-3T (because mine was >> 3T) >> 2. skullstripping brain mask using gcuts >> 3. adding control points (only on the left hemisphere) >> 4. recon-all -autorecon2-cp >> and this figure was made by a commnad line, [tkmedit wm.mgz -aux >> brain.mgz -surfs]. >> Best, >> EK. >> >> 2012/10/10 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> what was the name of the file that you transferred? >> On Wed, 10 Oct 2012, EK Kim wrote: >> >> I already uploaded this problem 2 days >> ago, reprocessing the subject to make >> sure about control points. >> However when I added the control points >> to the left hemisphere, >> the right hemisphere surface was changed >> severely. >> I used the command line, recon-all >> -autorecon2-cp -s subjectID. >> Could you tell me why does it occur and >> how to deal with it? >> >> >> Best, >> >> EK >> >> >> >> >> 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<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(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >>

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talairach.xfm error frequency
by Eric Cunningham 12 Oct '12

12 Oct '12

Greetings, I am trying to determine how bad a talairach.xfm registration has to be to warrant a manual edit. I have found that even minor edits can have noticable (9%) effects on major subcortical volumes (such as thalamus or hippocampus). Very few registrations seem to have completely failed, but most seem like they could be made better by a tweak here or there. At what point would I just be adding randomness by manually editing? About what percent of a given dataset would you expect to manually edit? Much appreciated, -Eric Cunningham

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Re: [Freesurfer] volumes per lobe
by MAHINDA YOGARAJAH 12 Oct '12

12 Oct '12

Dear Experts, As an addendum to the last post I made here are the commands I propose to use to extract lobar measures for GM and WM. I would be grateful for input. GM Lobar Values (1) mri_annotation2label --subject subject1 --hemi ?h --lobesStrict lobesfile (2) mri_anatomical_stats –mgz –cortex ../label/?h.cortex.label –f ../stats/?h.lobesfiles.stats –b –a ../label/?h.lobesfile.annot subject1 ?h white Q: Is this valid? Q:Do I need to include that part of the command in italics - is it not redundant given the use of the ?h.lobesfile.annot - using one or the other does give a different result at the top of the stats file (namely NumVert, WhiteSurfArea, and mean thickness which disappears if ?h.cortex.label is not passed) - why is this ? WM Lobar Values (1) mri_annotation2label --subject subject1 –hemi ?h --lobesStrict lobesfile (2) mri_aparc2seg --s subject1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.lobar.mgz --ctxseg aparc+aseg.mgz --annot ?h.lobesfile.annot Q: Is this valid ? Q: Do I need all the items in italics - they are present in the recon-all logfile but not in some forum posts on similar topics. (3a) mri_segstats --seg mri/wmparc.lobar.mgz --sum stats/wmparc.lobar.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject1 --surf-wm-vol --surf-ctx-vol --totalgray --ctab newcolourtable --etiv OR (3b) mri_segstats --seg mri/wmparc.lobar.mgz --sum stats/wmparc.lobar.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/norm.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject1 --surf-wm-vol --ctab newcolourtable --etiv Q: Which of these should I be using - the latter is based on the recon-all log file, while the former is based on forum posts - what are the differences (as highlighted in italics). Thanks. Mahinda

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mri_ms_fitparms?
by dgw 12 Oct '12

12 Oct '12

Hi, >From the wiki (http://www.freesurfer.net/fswiki/mri_ms_fitparms) I can see that mri_ms_fitparms can accept and afi map. Can someone tell me what assumptions the -afi subcommand makes about the position of the afi map relative to the flash volumes? does it calculate everything in scanner coordinates, or do I need to register them to one another? Thanks, D

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Re: [Freesurfer] volumes per lobe
by MAHINDA YOGARAJAH 12 Oct '12

12 Oct '12

Dear FreeSurfer Experts, I write in regard to the posting on calculating GM measures on a lobar basis. I had a couple of quick questions: 1) Having derived a lobesfile using mri_annotation2label --subject <name> --hemi lh --lobesStrict lobesfile one uses mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.lobesfile.stats -b -a ../label/lh.lobesfile.annot subject lh white a) Why is the -cortex ../label/lh.cortex.label option needed ? I thought this is needed if one wants to pass cortical label for computing statisitcs across all of the cortex ? When I repeat the command without it the stats at the bottom of the lobar stats file are the same. However the total number of vertices and white surface area total at the top of the stats file are different and without the -cortex option the average thickness at the top disappears - why is this ? Should the cortex flag be included or not for lobar GM volumes b) Does the flag white refer to areas based on white matter in which case if one wants areas based on pial surface should pial flag be used ? 2) What would the approach be to get lobar measures as above but for white matter instead ? Thanks. Mahinda

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Question about inferior temporal lobe topological/control points anomalies
by pietro de rossi 11 Oct '12

11 Oct '12

Dear FreeSurfer users and developers, I'm getting very frequently some bilateral inferior temporal lobe topological/control points anomalies. I attach an example with and without segmentation on. It seems to me that they are not affecting the pial surface's shape (inferior aspect of right temporal lobe attached in first picture. Should I edit and rerun recon? Thank you very much Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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TRACULA trac-all -path ERROR
by Fernando Ventrice 11 Oct '12

11 Oct '12

Dear Freesurfer-Tracula users, I'm trying to use Tracula to analyze some DTI images. I already used Freesurfer and FSL without problems. First of all, my system is the following: Linux Xubuntu 12.04 LTS x86_64 - Intel i7 - 8Gb RAM - Nvidia GeForce GT 520 1GB Freesurfer version 5.1.0 (freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz) FSL version 5.0.1 (from Neurodebian) The first problem I had was with the first command: "trac-all -prep -c dmrirc_file" gave an error about not finding the 'job' command. This was solved (thanks to Anastasia Yendiki) using: "set runlist=(1)" in the 'dmrirc_file'. Then, I had some problems with the second command: "trac-all -bedp -c dmrirc_file", which gave this error: Queuing preprocessing stages /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 216: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 263: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 321: [: xbedpostx_pre: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 458: [: x: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 472: [: -le: argument expected Queuing parallel processing stage /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 216: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 321: [: xbedpostx: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 458: [: x43: unexpected operator 0 slices processed Queuing post processing stage /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 216: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 263: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 321: [: xbedpostx_post: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 458: [: x: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 472: [: -le: argument expected Reading about this on the freesurfer mailing-list I got to the conclusion of running directly: bedpostx /home/labneuroimg/STATION_FLENI/Tensores/subject/TRACULA/subject/dmri (in the middle I learned how to use condor!) It finished without errors. So I went to the last command: "trac-all -path -c dmrirc_file" which complained about not finding the following file: ERROR: Could not open /home/labneuroimg/STATION_FLENI/Tensores/subject/TRACULA/subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt These files were at "/home/labneuroimg/STATION_FLENI/Tensores/subject/TRACULA/subject/dlabel/mni"... should I copy them to the diff folder?? I send as attachments the error output from "trac-all -path -c dmrirc_file" and the "dmrirc_file" I used. Best regards and thanks a lot! Fernando Ventrice El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. http://www.fleni.org.ar

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TRACULA: multiple bvecs files in one configuration file
by Loi 11 Oct '12

11 Oct '12

Hello, I see in the message thread that as of July 2011 there was no support for multiple bvecs files in one configuration file. Have any changes been made regarding this? And if so, how can I include multiple paths to bvecs files? Thank you, Joy-Loi

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Which atlas to use for optimal parcellation of the auditory cortex (HG and of the PT )?
by Narly Golestani 11 Oct '12

11 Oct '12

Dear all, dear Christophe Destrieux, 1. I would like to know which is the best version of freesurfer to use, or rather regarding the best atlas to call (using a flag) in order to ensure that our parcellation of the auditory cortex, and of the first transverse temporal gyrus and of the planum temporale in particular, are optimal. I see in an email dated Jan 3rd of this year that it was suggested to use the 2009 atlas for this. Is this still the best option to use? 2. and..: Can I invoke this by using the ‘--annot aparc.a2009s’ flag when writing the results to a table after having run recon-all –all using freesurfer version 4.4? If I’m not mistaken, version 4.4 does not generate the 2009 atlas, and I will need to instead run a more recent version of freesurfer. Thanks in advance for any input that you may have, Best wishes, Narly.

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