Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

overlapping surfaces after running recon-all
by Deirdre O Shea 02 Nov '12

02 Nov '12

Hello FreeSurfer experts, I am having a lot of trouble with the surfaces on some of my subjects. The main problem is that I am getting an overlap of the surfaces which can be clearly seen in the coronal view (see attached for an example). This has happened with several subjects even using different commands. One of the commands I used which produced this result was "recon-all -autorecon2-cp -autorecon3 -noaseg subjid (subject)". The other command i used which also produced these results was "recon-all -autorecon-pial -noaseg subjid (subject)" I was using the -noaseg flag after I was deleting some of the segmentation voxels that extended out from the cerrebellum as this was also a common edit. This was specified in the tutorial. Is this the correct procedure? I'm thinking maybe the problem I'm seeing is related to this flag. I hope someone can help. Best Regards, Deirdre

2 1

Compiling on Linux PPC
by Tony Dale 01 Nov '12

01 Nov '12

Hi, Does anyone have any advice for compiling freesurfer on Linux powerPC architectures? I've managed to compile a 64-bit version of freesurfer on Linux PowerPC, and I'd be happy to post the documentation for the compile process I used - if I could be sure it would build usable binaries :-( So far, the compiled binaries run in to some fairly basic problems with opening DICOM files. Here's an example using mri_probedicom with the debugging cranked up, trying to open a file that opens fine using the precompiled x86 mri_probedicom binary: # mri_probedicom --i /tmp/s003/E16002S003I00001.dcm DCM Dump Elements Object type: UNKNOWN Object size: 132 DCM Dump Elements Complete Starting DCM_CloseObject DCM_CloseObject: Legal object and file closed 0008 0005 CS 0 000008 ID Specific Character Set newElementItem: CTN_MALLOC 0 152 36214390 5349 5f4f UN 0 000010 newElementItem: CTN_MALLOC 0 152 36214430 3030 0008 UN 0 000018 newElementItem: CTN_MALLOC 0 152 36214540 DCM Dump Elements Object type: ELEMENT LIST Object size: 24 Group: 0008, Length: 8 0008 0005 0 // ID Specific Character Set// Group: 5349, Length: 8 5349 5f4f 0 // //DCM Dump Elements Complete Starting DCM_CloseObject DCM_CloseObject: Legal object and file closed DCM_CloseObject: group 0008 DCM_CloseObject: Element 00080005 DCM_CloseObject: free 36214390 DCM_CloseObject: group 5349 DCM_CloseObject: Element 53495f4f DCM_CloseObject: free 36214430 0800 0500 UN 0 000008 newElementItem: CTN_MALLOC 0 152 36214390 4953 4f5f UN 0 000010 newElementItem: CTN_MALLOC 0 152 36214430 3030 0800 UN 0 000018 newElementItem: CTN_MALLOC 0 152 36214540 DCM Dump Elements Object type: ELEMENT LIST Object size: 24 Group: 0800, Length: 8 0800 0500 0 // //Group: 4953, Length: 8 4953 4f5f 0 // //DCM Dump Elements Complete Starting DCM_CloseObject DCM_CloseObject: Legal object and file closed DCM_CloseObject: group 0800 DCM_CloseObject: Element 08000500 DCM_CloseObject: free 36214390 DCM_CloseObject: group 4953 DCM_CloseObject: Element 49534f5f DCM_CloseObject: free 36214430 Starting DCM_CloseObject ERROR: /tmp/s003/E16002S003I00001.dcm is not a dicom file or some other problem Entering IsDICOM (/tmp/s003/E16002S003I00001.dcm) Opening /tmp/s003/E16002S003I00001.dcm as part10 DCM Dump Elements Object type: UNKNOWN Object size: 132 DCM Dump Elements Complete DCM_FILEOPENFAILED 20092 DCM failed to open file: /tmp/s003/E16002S003I00001.dcm in DCM_OpenFile Starting DCM_CloseObject DCM_CloseObject: Legal object and file closed Opening as littleendian 0008 0005 CS 0 000008 ID Specific Character Set newElementItem: CTN_MALLOC 0 152 36214640 5349 5f4f UN 0 000010 newElementItem: CTN_MALLOC 0 152 36214710 3030 0008 UN 0 000018 newElementItem: CTN_MALLOC 0 152 36214820 DCM Dump Elements Object type: ELEMENT LIST Object size: 24 Group: 0008, Length: 8 0008 0005 0 // ID Specific Character Set// Group: 5349, Length: 8 5349 5f4f 0 // //DCM Dump Elements Complete DCM_FILEOPENFAILED Starting DCM_CloseObject DCM_CloseObject: Legal object and file closed DCM_CloseObject: group 0008 DCM_CloseObject: Element 00080005 DCM_CloseObject: free 36214640 DCM_CloseObject: group 5349 DCM_CloseObject: Element 53495f4f DCM_CloseObject: free 36214710 Opening as bigendian 0800 0500 UN 0 000008 newElementItem: CTN_MALLOC 0 152 36214640 4953 4f5f UN 0 000010 newElementItem: CTN_MALLOC 0 152 36214710 3030 0800 UN 0 000018 newElementItem: CTN_MALLOC 0 152 36214820 DCM Dump Elements Object type: ELEMENT LIST Object size: 24 Group: 0800, Length: 8 0800 0500 0 // //Group: 4953, Length: 8 4953 4f5f 0 // //DCM Dump Elements Complete DCM_FILEOPENFAILED Starting DCM_CloseObject DCM_CloseObject: Legal object and file closed DCM_CloseObject: group 0800 DCM_CloseObject: Element 08000500 DCM_CloseObject: free 36214640 DCM_CloseObject: group 4953 DCM_CloseObject: Element 49534f5f DCM_CloseObject: free 36214710 Opening as format conversion DCM_ILLEGALOPTION Starting DCM_CloseObject Leaving IsDICOM (/tmp/s003/E16002S003I00001.dcm) ERROR: /tmp/s003/E16002S003I00001.dcm is not a dicom file or some other problem This email may be confidential and subject to legal privilege, it may not reflect the views of the University of Canterbury, and it is not guaranteed to be virus free. If you are not an intended recipient, please notify the sender immediately and erase all copies of the message and any attachments. Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more information.

2 2

Cropping/slicing surfaces & read in matlab
by octavian lie 01 Nov '12

01 Nov '12

I am able to load patch ok in tksurfer, however I get the following error message when trying to read the patch in Matlab. Attached you find the original surface (sub_), and its patch (inner-). Any help appreciated. Alternatively, you suggested to modify the ripflag=1 for the hemi to be left out, in this case for x<0, how would I do it in read_surf? fname_patch='/usr/local/freesurfer/subjects/sub/surf/rh.inner-skull-surface' fname_patch = /usr/local/freesurfer/subjects/sub/surf/rh.inner-skull-surface >> read_patch Attempted to access poly(1); index out of bounds because numel(poly)=0. Error in read_patch (line 41) numvert = poly(1); Thank you very much, Octavian

1 0

Re: [Freesurfer] Cropping/slicing surfaces
by octavian lie 01 Nov '12

01 Nov '12

Thank you, Bruce. Is seems that the cut works well in tksurfer, however I am unable to save the cut surface, if I use save or save as, it saves the original (whole) surface. What should I do? Octavian. On Thu, Nov 1, 2012 at 11:49 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > the easiest thing would be to copy it into surface as lh.bem then run > tksurfer on it > > On Thu, 1 Nov 2012, octavian lie wrote: > > Thank you for your quick prompt, how do I pull the inner skull surface >> into tksurfer, given it is in /bem and not in /surf, and >> does not have a lh or rh option? >> Octavian >> >> On Thu, Nov 1, 2012 at 11:41 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Octavian >> >> sure, define a sagittal cutting plane in tksurfer, or in matlab set >> ripflag=1 for all vertices with the x coord > 0 >> (or < 0) >> >> cheers >> Bruce >> On Thu, 1 Nov 2012, octavian lie wrote: >> >> Dear all, >> >> Is there a way to crop a surface in FS, freeview or matlab? I >> have the inner_skull_surface in BEM >> folder, and I want to see just >> the right half, akin to cropping along the A (RAS) axis from >> the left. This is in order to visualize the >> inside of the surface >> with some electrode applications. Also, if the surface can be >> created in MNE just on the right side that >> will solve it. >> Help much appreciated, >> Octavian Lie. >> >> >> >> >> 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. >> >> >> >>

2 5

recon-all finished with ERRORs
by Christine Smith 01 Nov '12

01 Nov '12

See my original post at the end of this message and some more information included below. What would have been edited between the previous run without errors and the current run with errors is the brainmask, the wm.mgz file, and control points. On Tue, Oct 30, 2012 at 1:21 PM, Christine Smith <cnsmith(a)ucsd.edu> wrote: > Here it is: > > New invocation of recon-all > > Thu Oct 4 03:52:22 PDT 2012 > /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 > /usr/local/freesurfer/bin/recon-all > -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel > #-------------------------------------- > #@# SubCort Seg Thu Oct 4 03:52:22 PDT 2012 > > mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz > > Linux squirelab.ucsd.edu 2.6.18-308.13.1.el5 #1 SMP Tue Aug 21 > 18:44:22 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s CON1 exited with ERRORS at Thu Oct 4 03:52:22 PDT 2012 > > On Tue, Oct 30, 2012 at 12:45 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: >> what were the last 20 lines or so of the recon-all.log? >> >> On Tue, 30 Oct 2012, Christine Smith wrote: >> >>> Hello, >>> >>> After successfully running a subject through freesurfer (recon-all >>> -make all) several times as I fixed some pial and white matter edits, >>> I now get the message that recon-all finished with errors. Inspection >>> of the recon-all.log doesn't reveal any error messages to me in any >>> particular step. >>> >>> What should I be looking for to track down the reason that errors were >>> generated? >>> >>> I already examined the talairach transform and that looks great. >>> I loaded the pial and white matter surfaces and they look fine. The >>> segmentation aparc+aseg looks great too. >>> >>> Thanks, >>> Christine >>> >>> >>

2 4

Cropping/slicing surfaces
by octavian lie 01 Nov '12

01 Nov '12

Dear all, Is there a way to crop a surface in FS, freeview or matlab? I have the inner_skull_surface in BEM folder, and I want to see just the right half, akin to cropping along the A (RAS) axis from the left. This is in order to visualize the inside of the surface with some electrode applications. Also, if the surface can be created in MNE just on the right side that will solve it. Help much appreciated, Octavian Lie.

2 1

Re: [Freesurfer] fieldsign-sess problem in retinotopy
by Zhou, Wei 01 Nov '12

01 Nov '12

Hi Doug, The subject name for structural is "SUBJ1" when I did recon-all, which is also the content of file "subjectname". My dir structures of "structural" and "retinotopy" are the same as http://www.alivelearn.net/?p=65 . "SUBJ1" is stored under "structural". if I set SUBJECTS_DIR as "....../structural", $SUBJECT_DIR/SUBJ1 does exist, then still I get the same error msg. The following is the log file: fieldsign-sess log file $Id: fieldsign-sess,v 1.2 2010/05/04 22:00:18 greve Exp $ Thu Nov 1 10:36:52 CDT 2012 Linux rii-appserv-02 2.6.32-279.11.1.el6.x86_64 #1 SMP Sat Sep 22 07:10:26 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux /media/users/zhouw4/testf/retinotopy /usr/local/freesurfer/fsfast/bin/fieldsign-sess -a rtopy.self.lh -occip -s SUBJ1 uid=20120(zhouw4) gid=22000(rii_users) groups=22000(rii_users),21100(rii_appservers),23000(domain^users) context=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 Best Wei >What is the name of FreeSurfer subject? This is not necessarily the same >> >as SUBJ01 in your command line below. That is the session (which may or >may not be the same as the "subject name"). What ever the subjectname is, does SUBJECT_DIR/subject exist? On 10/31/2012 03:07 PM, Zhou, Wei wrote: > > Hi, Doug > > Thank you for your reply. I have tried exporting SUBJECTS_DIR to the > directory of upper fold, retinotopy or SUBJ01 But none of them works. > Still the same error msg. > > So what should SUBJECTS_DIR be exported to for this analysis? > > Best > > Wei > > > > >Hi Wei, this is a bug in the error msg. It is trying to say that your > >source subject is not in the $SUBJECTS_DIR. > >doug > > >On 10/27/2012 02:27 PM, Zhou, Wei wrote: > > Dear freesurfers, > > > > I am trying retinotopy analysis in freesurfer. For "fieldsign-sess", I > > encounter the following problem when I type "fieldsign-sess -a > > rtopy.self.lh -occip -s SUBJ01" or "fieldsign-sess -a rtopy.self.lh > > -occip -sf sessid": > > > > */media/users/zhouw4/testf/retinotopy/SUBJ01/log/fieldsign-sess.log* > > *subject: Undefined variable.* > > > > my structure of retinotopy fold is : > > retinotopy > > | |--sessid > > |--SUBJ01 > > |--subjectname > > > > |--bold > > |--001 > > |--f.nii > > |--rtopy.par| > > > > I really appreciate it if you could give me some idea about that > > problem. Thanks a lot in advance. > > > > Best > > Wei Zhou > > Medical Physics Ph.D. Student > > Diagnostic Imaging Track > > cgxz...(a)gmail.com<mailto:cgxz...@gmail.com> > > zho...(a)livemail.uthscsa.edu<mailto:zho...@livemail.uthscsa.edu> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Best Wei Zhou Medical Physics Ph.D. Student cgxzwwd(a)gmail.com<mailto:cgxzwwd@gmail.com> zhouw4(a)livemail.uthscsa.edu<mailto:zhouw4@livemail.uthscsa.edu>

2 1

QA TOOL
by Efrat Kliper 01 Nov '12

01 Nov '12

Dear Freesurfer expert, I am using Freesurfer version 5.1.0. I am dealing with some problems with recon_checker command. I cannot open the html file to see the figures. The command generates the images but they are not saved. It is written that: *converting snapshots to tiff and making html page...* *Convert: command not found* Any suggestions? Thanks in advance, efrat

2 1

Re: [Freesurfer] fieldsign-sess problem in retinotopy
by Zhou, Wei 31 Oct '12

31 Oct '12

Hi, Doug Thank you for your reply. I have tried exporting SUBJECTS_DIR to the directory of upper fold, retinotopy or SUBJ01 But none of them works. Still the same error msg. So what should SUBJECTS_DIR be exported to for this analysis? Best Wei >Hi Wei, this is a bug in the error msg. It is trying to say that your >source subject is not in the $SUBJECTS_DIR. >doug >On 10/27/2012 02:27 PM, Zhou, Wei wrote: > Dear freesurfers, > > I am trying retinotopy analysis in freesurfer. For "fieldsign-sess", I > encounter the following problem when I type "fieldsign-sess -a > rtopy.self.lh -occip -s SUBJ01" or "fieldsign-sess -a rtopy.self.lh > -occip -sf sessid": > > */media/users/zhouw4/testf/retinotopy/SUBJ01/log/fieldsign-sess.log* > *subject: Undefined variable.* > > my structure of retinotopy fold is : > retinotopy > | |--sessid > |--SUBJ01 > |--subjectname > > |--bold > |--001 > |--f.nii > |--rtopy.par| > > I really appreciate it if you could give me some idea about that > problem. Thanks a lot in advance. > > Best > Wei Zhou > Medical Physics Ph.D. Student > Diagnostic Imaging Track > cgxz...(a)gmail.com <mailto:cgxz...@gmail.com> > zho...(a)livemail.uthscsa.edu <mailto:zho...@livemail.uthscsa.edu> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

2 1

Error during recon-all with notal-check on
by Darshan P 31 Oct '12

31 Oct '12

I have a MRI data which has a lesion on the left side . recon-all fails with errors . I was hoping to recover from this error . The last few lines of the log file is as follows'

1 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