Freesurfer April 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
229 discussions

Re: [Freesurfer] Standard surface tessellation
by Chris McNorgan 04 Apr '14

04 Apr '14

Hi Justin, This is quite similar to a question I had asked previously: https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33421.html I believe the solution is to generate a 14000 vertex template, and then appy mri_surf2surf to all 10 subjects, which will map the vertices of all 10 subjects to your template. The 10 transformed surfaces should then correspond with one another. Chris Subject: [Freesurfer] Standard surface tessellation From: jeongwon(a)pet.wayne.edu Date: 14-04-03 03:47 PM To: freesurfer(a)nmr.mgh.harvard.edu Dear FreeSurfer, I am a beginner in FreeSurfer and wonder if it is possible in FreeSurfer to apply the same triangulation across multiple subjects, i.e. the same number of vertices and triangles at the anatomically identical locations. For instance, I have 10 subjects and want to have pial (or white matter) surfaces of individual subjects consisting of 14000 vertices which are anatomically matched. Any suggestion will be greatly appreciated. Justin.

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Subcortical segmentation for PAG
by Jeni Chen 03 Apr '14

03 Apr '14

Hi, Just wondering if the periaqueductal gray is part of the automatic segmentation process and if we can obtain the volume. I checked the aseg table but didn't see it, however, I somehow remember seeing it before... Was it ever included? Thanks. Jeni

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Standard surface tessellation
by jeongwon＠pet.wayne.edu 03 Apr '14

03 Apr '14

Dear FreeSurfer, I am a beginner in FreeSurfer and wonder if it is possible in FreeSurfer to apply the same triangulation across multiple subjects, i.e. the same number of vertices and triangles at the anatomically identical locations. For instance, I have 10 subjects and want to have pial (or white matter) surfaces of individual subjects consisting of 14000 vertices which are anatomically matched. Any suggestion will be greatly appreciated. Justin.

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missing Freesurfer wiki pages
by Gabor Perlaki 03 Apr '14

03 Apr '14

Dear all, Most of the links on https://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction page do not work. If I clik for example on FsTutorial/SkullStripFix the following message will popup: "This page does not exist yet. You can create a new empty page, or use one of the page templates." Is there a new page for the recommended workflow which works fine? Thanks, Gabor

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preprocessing question
by Eiran Harel 03 Apr '14

03 Apr '14

Dear freesurfers, I have installed freesurfer and fsl on my Mac: -------- freesurfer-Darwin-snowleopard-i686-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 I am trying to run Preproc-sess command: preproc-sess -s bsmt102 -surface fsaverage lhrh -mni305 -fwhm 5 -fsd bold -stc odd -per-run -force and get this error: mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 ERROR: cannot find either fslmaths for avwmaths Any suggestions? Thanks! Eiran [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_01.jpg]<http://www.tasmc.org.il/be-well/Pages/default.aspx> [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_02.jpg] <https://www.facebook.com/ichilov.medical> [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_03.jpg] <http://twitter.com/tasmc1> [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_04.jpg] <http://www.youtube.com/tasmc1> [http://www.tasmc.org.il/DocLib/SIGN/sign_smallEN_05.jpg] <http://www.tasmc.org.il/sites/en/Pages/default.aspx>

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normalization problem
by Gregory Kirk 03 Apr '14

03 Apr '14

Hi, i ran about 260 subjects and got good results for all but 30. the 30 that failed all seemed to have the same problem with normalization. the original were done with v5.1 i reran one with 5.3 and the problem was reduced. I attached a slice of the T1 from each. the 5.3 rerun produced a good quality brainmask.mgz, the originalrun with 5.1 failed to produce the brainmask.mgz the original orig.mgz volumes look fairly decent, they were aquired on a good 1.5T scanner. since it ran much better on 5.3 im thinking some defaults were changed and perhaps i can add some flags with new default values to get 5.1 to produce usable results, i.e. the 230 other subjects have been inspected and im thinking they really really don't want to reinspect all of them after running on 5.3 can you suggest options/flags that i can try to rerun with 5.1 thanks greg

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Re: [Freesurfer] LGI - Statistical Analysis
by Marie Schaer 03 Apr '14

03 Apr '14

Hi Kenza, (I added the freesurfer mailing list in copy, please post there) You have to set the min threshold at 1 when you overlay the lGI, then you should not see any gray regions anymore. Not sure I understood your problem with the statistical analyses, maybe there is simply no significant difference? If you could complete the lGI without problem (which is the case if you have the ?h.pial_lgi files), and if you are certain of your statistical design, then it simply means that there is nothing which is more significant than the given significance threshold (you can play with the significance threshold to explore that as well, and visualize the data in plots at some vertices in qdec). Best, Marie On Apr 3, 2014, at 4:57 AM, Kenza Drissi-kaÃ¯touni <kenza.drissi-kaitouni(a)polymtl.ca> wrote: > > > Dear Marie, > > I have been trying to use the lgi implemented in Freesurfer. I was able to > obtain results, but unfortunately, when I overlay visualize them as an overlay > of ?h.pial_lgi on the ?h.pial surface in tksurfer, I still see gray regions > which shouldnt be... What can I do to fix this problem? > > Also, when I perform a statistical analysis on the data I obtained, only 2 small > spots appear for lh and none for rh. I strongly suspect this is because of the > gray regions where no lgi was apparently calculated/retained. Is it so? > > Thank you very much for you time, > Kenza Drissi-Kaitouni > B.Sc. Biomedical Engineering > Ecole Polyetchnique de Montreal > > D.E.S.S Biomedical Engineering >

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Inconsistent results of the same subjects from different Freesurfer processing
by Zixuan Yang 02 Apr '14

02 Apr '14

Dear FreeSurfers, I have been processing a group of subjects, firstly using Freesurfer V5.1.0 or V5.3.0, then V5.3.0 after making some editing on WM and pial surface, using the <recon-all> command, without the <-no-isrunning> option. I have below message at the beginning of the recon-all after editing: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/zixuan/Work/FS/RE_EDIT Actual FREESURFER_HOME /usr/share/freesurfer -rw-r--r--. 1 zixuan users 957929 Dec 20 16:52 /home/zixuan/Work/FS/RE_EDIT/D3358/scripts/recon-all.log Linux NIL.Melbourne 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/share/freesurfer Previous: /share/apps/freesurfer/5.3.0 #-------------------------------------------- #@# Mask BFS Wed Apr 2 17:11:43 EST 2014 /home/zixuan/Work/FS/RE_EDIT/D3358/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz However all subjects have been finished without error, which is not the case as what you have discussed in the mail archive. recon-all -s <subjID> finished without error at Mon Mar 24 03:38:36 EST 2014 The problem is, I found the cortical thickness in regions that I didn't edit not consistent before and after re-processing, with about 2-10% differences. For some subjects, I have only edited minor pial surface (e.g. entorhinal cortex only), yet it seems that all values have been affected. My question is 1), shall I consider my results valid, despite of the "dismatch" thing? Is there any other factors other than editing will affect the final value? 2), I have about 30 subjects processed with V5.1.0, (atrophic brain +++ with heavy editing - extreme time consuming), yet I still found some pial to edit this time, and processed them with V5.3.0. Shall I consider the values valid provided the message "without error", despite the different FreeSurfer versions? Apologies for cross posting, I didn't found any cases similar to mine in the mail archive. Many thanks and kind regards, Zixuan -- Zixuan YANG Ph.D candidate Centre for Healthy Brain Ageing (CHeBA) School of Psychiatry, UNSW Medicine NPI, Euroa Centre, Barker Street, Randwick NSW 2031 AUSTRALIA T: +61 (2) 9385 0427 W: www.cheba.unsw.edu.au<http://www.cheba.unsw.edu.au/> E: z.yang(a)student.unsw.edu.au<mailto:s.reppermund@unsw.edu.au> ______________ Mailing address: University of New South Wales Randwick Campus, Building R1f 22-32 King Street, Randwick NSW 2031 Australia

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FW: registration difficulty
by Erik O'Hanlon 02 Apr '14

02 Apr '14

Dear FS experts, I am running my first FS analysis and I'm trying to register my hippocampal subdivision volumes to my diffusion space image but cannot get good alignment. I ran my diffusion preprocessing in ExploreDTI so don't have the register.dat file automatically so created this using the bbregister tool and registered B0 image to my orig.mgz. I then used this dat to align my aseg to my diffusion space image and it worked well. The issue is when I try to use it to transform my hippocampal subfield volumes to diffusion space. They just don't line up. Is this due to the different FOV for the subfields? Can anyone advise how to get these volumes to transform correctly? Any help would be greatly appreciated. Thanks Erik Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE

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Re: [Freesurfer] quality T1 scans for new study
by Andre van der Kouwe 02 Apr '14

02 Apr '14

No, I think that's a reasonable protocol to use and good to use SENSE to speed it up. -------- Original message -------- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date:04/01/2014 2:28 PM (GMT+02:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Cc: Andre van der Kouwe <andre(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] quality T1 scans for new study looks pretty reasonable. Andre: any comments/suggestions? On Tue, 1 Apr 2014, Kok, JG (neuro) wrote: > Hi Bruce, > > Thanks for your fast reply. > > Hereby I attach the parameter files of both scans (although I suspect looking at the parameters of "scan1" may be sufficient). Checking it with the information on Philips at "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pr…": > > " > Sequence: T1W_3D_TFE_SENSE > Acquisition time: 5:13 > Voxel size: 1.0 x 1.0 x 1.0 mm3 > Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness 1 mm, (3D encoding) > Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth 191.5 Hz/px > RF: flip angle 7° > Acceleration: 2x SENSE > " > > suggests that parameters in "scan1_parameter_file.txt" are already pretty similar to those I guess. (Is it the SENSE that is missing in our protocol that is the most important difference?) > > Thanks, > > Jelmer > > ________________________________________ > Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] namens Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Verzonden: dinsdag 1 april 2014 14:09 > Aan: Freesurfer support list > Onderwerp: Re: [Freesurfer] quality T1 scans for new study > > Hi Jelmer > > if you give us the specific acquisition details we can help more (receive > coil, acceleration, voxel size, sequence type, TR/TE/TI/flip > angle/bandwidth, etc....). We also have recommended morphometry sequences > on our website. > > 10 min is a pretty long structural scan for a modern MRI scanner. > > cheers > Bruce > > On Tue, 1 Apr 2014, > Kok, JG (neuro) wrote: > >> Dear Freesurfer experts, >> We are planning to start a new MRI study which will include T1 scans. As we >> are in a testing phase now, I was wondering whether you could comment on the >> attached screenshots. Clearly, "scan1" has a better white matter/grey matter >> contrast than "scan2". Do you think going for "scan1" would be the sensible >> thing to do when we later wish to use Freesurfer with these scans? Or >> perhaps is neither of the examples I attached good enough? >> >> By the way, these scans were acquired on a Philips 3T scanner, both taking >> around 10 minutes. >> >> It you need any more information, please let me know. Many thanks in advance >> for your advice. >> >> Jelmer Kok >> >> ____________________________________________________________________________ >> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de >> geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken >> van dit bericht, het niet openbaar maken of op enige wijze verspreiden of >> vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een >> incomplete aankomst of vertraging van dit verzonden bericht. >> >> The contents of this message are confidential and only intended for the eyes >> of the addressee(s). Others than the addressee(s) are not allowed to use >> this message, to make it public or to distribute or multiply this message in >> any way. The UMCG cannot be held responsible for incomplete reception or >> delay of this transferred message. >> > _______________________________________________ > 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. > > ________________________________ > De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. > > The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. >

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Freesurfer April 2014