Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

Re: [Freesurfer] wm.mgz
by Xiaomin Yue 25 Jul '14

25 Jul '14

Thanks. I will replace 0 with 1. Xiaomin ________________________________ From: Bruce Fischl<mailto:fischl@nmr.mgh.harvard.edu> Sent: ‎7/‎25/‎2014 9:43 PM To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] wm.mgz Yes, they won't be preserved unless they are 1 > On Jul 25, 2014, at 9:33 PM, Xiaomin Yue <yuexm(a)hotmail.com> wrote: > > It is 5.3. The voxels erased was set as 0. Is that the problem? If so, I can try to replace 0 with 1. > > Xiaomin > From: Bruce Fischl > Sent: ‎7/‎25/‎2014 9:22 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] wm.mgz > > What version? Check the voxels you erased and see if they were set to 1 instead of 0 > > On Jul 25, 2014, at 8:39 PM, Xiaomin Yue <yuexm(a)hotmail.com> wrote: > >> Hi Bruce, >> >> Thanks for your response. the editing was done in freeview. I saved the edited version as wm.edited.mgz, then copy the wm.edited.mgz to wm.mgz. is that the problem? Is it necessary to save the edited wm.mgz as wm.mgz in freeview? I hope it is clear what I did. >> >> Thanks, >> Xiaomin >> >> From: Bruce Fischl >> Sent: ‎Friday‎, ‎July‎ ‎25‎, ‎2014 ‎8‎:‎36‎ ‎PM >> To: Freesurfer support list >> >> Hi Xiaomin >> >> how did you edit wm.mgz? If within tkmedit (or "recon editing" in freeview) >> and you reran recon-all it should have preserved your edits, even though it >> regenerated the file. Have you checked? >> >> Bruce >> >> >> On Fri, 25 Jul 2014, Xiaomin Yue wrote: >> >> > Hi, >> > >> > My edited wm.mgz was saved as wm.edited.mgz, then it copied to wm.mgz. I re-run the anlysis using >> > recon-all -s cologna -autorecon2-wm. From some reason, the analysis regenerated wm.mgz from brain.mgz, >> > which of course replaced my edited wm.mgz. Did I do some wrong here? >> > >> > Thanks, >> > Xiaomin >> > >> > >> _______________________________________________ >> 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 _______________________________________________ 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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Re: [Freesurfer] wm.mgz
by Xiaomin Yue 25 Jul '14

25 Jul '14

It is 5.3. The voxels erased was set as 0. Is that the problem? If so, I can try to replace 0 with 1. Xiaomin ________________________________ From: Bruce Fischl<mailto:fischl@nmr.mgh.harvard.edu> Sent: ‎7/‎25/‎2014 9:22 PM To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] wm.mgz What version? Check the voxels you erased and see if they were set to 1 instead of 0 > On Jul 25, 2014, at 8:39 PM, Xiaomin Yue <yuexm(a)hotmail.com> wrote: > > Hi Bruce, > > Thanks for your response. the editing was done in freeview. I saved the edited version as wm.edited.mgz, then copy the wm.edited.mgz to wm.mgz. is that the problem? Is it necessary to save the edited wm.mgz as wm.mgz in freeview? I hope it is clear what I did. > > Thanks, > Xiaomin > > From: Bruce Fischl > Sent: ‎Friday‎, ‎July‎ ‎25‎, ‎2014 ‎8‎:‎36‎ ‎PM > To: Freesurfer support list > > Hi Xiaomin > > how did you edit wm.mgz? If within tkmedit (or "recon editing" in freeview) > and you reran recon-all it should have preserved your edits, even though it > regenerated the file. Have you checked? > > Bruce > > > On Fri, 25 Jul 2014, Xiaomin Yue wrote: > > > Hi, > > > > My edited wm.mgz was saved as wm.edited.mgz, then it copied to wm.mgz. I re-run the anlysis using > > recon-all -s cologna -autorecon2-wm. From some reason, the analysis regenerated wm.mgz from brain.mgz, > > which of course replaced my edited wm.mgz. Did I do some wrong here? > > > > Thanks, > > Xiaomin > > > > > _______________________________________________ > 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.

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Re: [Freesurfer] wm.mgz
by Xiaomin Yue 25 Jul '14

25 Jul '14

Hi Bruce, Thanks for your response. the editing was done in freeview. I saved the edited version as wm.edited.mgz, then copy the wm.edited.mgz to wm.mgz. is that the problem? Is it necessary to save the edited wm.mgz as wm.mgz in freeview? I hope it is clear what I did. Thanks, Xiaomin From: Bruce Fischl Sent: ‎Friday‎, ‎July‎ ‎25‎, ‎2014 ‎8‎:‎36‎ ‎PM To: Freesurfer support list Hi Xiaomin how did you edit wm.mgz? If within tkmedit (or "recon editing" in freeview) and you reran recon-all it should have preserved your edits, even though it regenerated the file. Have you checked? Bruce On Fri, 25 Jul 2014, Xiaomin Yue wrote: > Hi, > > My edited wm.mgz was saved as wm.edited.mgz, then it copied to wm.mgz. I re-run the anlysis using > recon-all -s cologna -autorecon2-wm. From some reason, the analysis regenerated wm.mgz from brain.mgz, > which of course replaced my edited wm.mgz. Did I do some wrong here? > > Thanks, > Xiaomin > > _______________________________________________ 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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mri_edit_wm_with_aseg details
by Mark Plantz 25 Jul '14

25 Jul '14

Hi freesurfers, I am having an issue using 'mri_edit_wm_with_aseg' with a non-default atlas. The wm.seg.mgz file looks OK, but when combined with the aseg.mgz file to create wm.asegedit.mgz, incorrect regions are being filled. Could this be due to the fact that my atlas has non-default labels (i.e. right-cerebral-wm is labeled 140 instead of 41 in the default atlas)? Or would that not make a difference? I attached screenshots of both wm.seg and wm.asegedit. Thank you! -MP

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Convert volume 2 Label
by Bastian Cheng 25 Jul '14

25 Jul '14

Dear Freesurfer-Experts, Is there an automated way to convert an overlay volume to a label file? I guess I would look for a command called "vol2label". I am currently projecting volume files (fMRI activiation hotspots) to surfaces (mri_vol2surf): this works nicely. However I then would have to define labels manually (using "custom fill") by clicking on all (unconnected) spots on my surface. Please excuse any redundancies, I have not found a good solution in the forum yet. Best regards, Bastian.

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RA position available in Neuroimaging of Multiple Sclerosis
by Lilla Zollei 25 Jul '14

25 Jul '14

Contact Caterina Mainero, M.D. (caterina(a)nmr.mgh.harvard.edu) if interested! >>> A full-time Research Technologist (Assistant) position is available in the field of Neuroimaging of Multiple Sclerosis (MS) at the A. A. Martinos Center for Biomedical Imaging of Massachusetts General Hospital (MGH). Duties will include acquiring and analyzing positron emission tomography (PET), functional magnetic resonance imaging (fMRI), diffusion tensor imaging (DTI) and high-resolution morphometric data acquired at high-field (3T) and ultra-high-field (7T) MRI in studies of patients with MS. The central research program seeks to study brain pathology in subjects with multiple sclerosis, and to identify in vivo bio-imaging markers that could help to improve monitoring multiple sclerosis disease course and potentially response to treatments. To investigate this, our laboratory utilizes ultra-high-field MRI and a multimodal imaging acquisition approach, together with an extensive clinical and cognitive assessment of patients. We collaborate with an interdisciplinary group of clinicians, psychologists and neuroscientists to accomplish our research objectives. The responsibilities of the Research Assistant position are varied, and involve all phases of human neuroimaging research. Specifically, the position involves the collection, management and analysis of multiple modes of imaging and requires the processing of functional, structural MRI and behavioral data. Requirements Undergraduate or Master degree in Physics and/or Biomedical Engineering, Computer Science or related field. Written and oral English communication skills are required. Solid PC-based skills are needed in word processing, spreadsheet and presentation programs. Proficiency in statistics and programs such as SPSS, or R are especially desirable. The ideal candidate would also have strong experience with MATLAB and UNIX/LINUX. Candidates with prior experience in neuroimaging research will be given special consideration. The job requires a candidate who is mature, responsible and flexible with strong interpersonal skills. The candidate must have excellent organizational skills and be able to maintain accurate records. The environment can be fast-paced and calls upon the individual to independently problem-solve/trouble-shoot, prioritize multiple tasks and seek assistance when appropriate. Interested applicants should send a cover letter describing research experience, interests and goals, as well as a curriculum vitae with contact names and details of three references to: Caterina Mainero, M.D., by e-mail: caterina(a)nmr.mgh.harvard.edu. A two-year time commitment is requested and salary will be based on qualifications and experience. The Massachusetts General Hospital is an Equal Opportunity/Affirmative Action Employer.

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WM inspection with freeview
by Pablo Najt 25 Jul '14

25 Jul '14

Dear FS experts, I have a doubt about inspecting white matter with free view. I could not find any irregularities where the blue line cuts through the surface. However, I noted in a few areas that the pail border makes funny shapes and seems to close up (please see attaches). I am in doubt here whether this should be edited or not. I have checked this in the other views and the inflated surface but I could not find anything wrong with the scan (eg.. a dimple or a hole). So I wanted to enquire whether I should consider this as a potential issue for editing. Also in the last attachment I have doubts about a yellow coloured in right parietal area apron. in the border between the white and pial. I was surprised of the location of this as the ventricles are usually yellow. It might be nothing but I just wanted to double check. Thank you! Pablo

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qcache number of vertices error [fixed]
by O'Shea,Andrew 25 Jul '14

25 Jul '14

Hello all, I was able to fix my error (see below) by re-running recon-all $SUB –autorecon2 –autorecon3 –qcache . However I am unsure why –make all was not incorporating edits correctly? Is it inappropriate to use –make all after manual edits? If so, should I just use –autorecon2 –autorecon3 as a catch all (assuming no edits in the first stage) after manual edits? -Andrew ----- Hello, I am running into an error when using qcache. Subjects that have had manual edits are exited with errors, while subjects that have not had edits run fine. All subjects have had –make all ran after edits and finished without errors. I have read about this problem and tried some of the solutions but am still getting errors. When I first tried running –qcache I received this error: Reading curvature file /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.volume ERROR: number of vertices in /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.volume does not match surface (128222,130849) ERROR: reading curvature file Linux c2a-s21.ufhpc 2.6.32-358.23.2.el6.x86_64 #1 SMP Sat Sep 14 05:32:37 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1492 exited with ERRORS at Wed Jul 23 10:32:24 EDT 2014 To make sure everything was ran I re-ran –make all and got make: Nothing to be done for `all’. I then ran –vno_match_check and it said everything was fine: Pass: all surfaces and surface data for subject 1492 for hemi lh have the same number of vertices. Pass: all surfaces and surface data for subject 1492 for hemi rh have the same number of vertices. I saw Doug gave this suggestion ( using –surf volume –qcache) to someone who was having the same problem this resulted in qcache getting past the volume stage but failing lh.w-g.pct.mgh Reading curvature file /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.w-g.pct.mgh ERROR: number of vertices in /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.w-g.pct.mgh does not match surface (128222,130849) ERROR: reading curvature file Linux c1a-s11.ufhpc 2.6.32-358.23.2.el6.x86_64 #1 SMP Sat Sep 14 05:32:37 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1492 exited with ERRORS at Wed Jul 23 11:07:01 EDT 2014 Any suggestions on how to address this? Any idea of the cause? I assuming it has something to do with the manual edits since unedited ppl run fine. -Andrew

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Serious error in updating ?h.aparc.stats in FLAIR/T2pial processing pipeline
by Martijn Steenwijk 24 Jul '14

24 Jul '14

Dear all, It seems that there is a serious error in the Parcellation stats files (i.e. ?h.aparc.stats) when using the FLAIR / T2 processing pipeline of FS 5.3. starting a particular recon-all with recon-all -s ${SUBJID} -i ${DIR} -FLAIR ${DIR/t1/flair} -FLAIRpial -all and looking through the recon-all.cmd file, it appears that the Parcellation stats are computed prior to refining the pial surfs, but not updated after refining the pial surfs. For instance: #@# Parcellation Stats lh Thu May 29 14:36:50 CEST 2014 and further on: #@# Refine Pial Surfs w/ T2/FLAIR Thu May 29 15:36:58 CEST 2014 but mris_anatomical_stats is not called again after updating the pial surfs. This can also be recognized by comparing the last-modified times of lh.aparc.stats and lh.pial-files, where the time of the first is older than compared to the latter. Moreover the ?h.aparc.stats of separate freesurfer runs with and without pial surface correction are *identical*. Is this a known issue? Best, Martijn

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Deep white matter parcellated atlas
by Alshikho, Mohamad J. 24 Jul '14

24 Jul '14

Hi Dear Fs Experts, I am looking for an atlas segmented all white matter without to leave any unsegmented white matter like in WMPARC I highly appreciate your help and support Thanks Mohamad

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Freesurfer July 2014