Freesurfer

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21 participants
30071 discussions

Stats per region to brain map
by Johannes Klene 17 Feb '17

17 Feb '17

Hi! I've been reading up on tkviewer etc. but can't figure out how to accomplish the following: I calculated some stats (outside Freesurfer) summarizing the relation between cortical thickness and my outcome measure, per region present in the Killiany/Desikan atlas (i.e. running analyses on data obtained from aparcstats2table). Now I'd like to visualize these results, one number per region, by projecting them on the standard brain such that regions that showed a stronger association are more yellow and regions with weaker association are more red. Is there a straightforward way of doing this? I was thinking of maybe adjusting the RGB values in FreeSurferColorLUT.txt file? I'd be very grateful if anyone can provide some tips how to handle this. Kind regards, Johannes

2 4

Parallelization not working as implemented
by Francis Tyson Thomas 17 Feb '17

17 Feb '17

Hi, I have run recon-all with both -parallel enabled (including different openmp threads) and disabled and I'm not able to get processing times same as the information provided in recon-all help. The CPU used is *Dual Intel **Xeon E5-2623 v3* paired with 32GB DDR4 RAM. Is the configuration presented in recon-all help a dual cpu configuration? Following are the runtimes I have obtained, no parallelization : 7 hrs and 58 mins -parallel (coarse parallelization) : 4 hrs and 39 mins -parallel (fine parallelization; -openmp 8) : 4 hrs and 34 mins -parallel (fine parallelization; -openmp 14) : 4 hrs and 37 mins Somehow varying the number of threads is having no effect in the execution time of recon-all as can been seen from the processing times. If you can explain what could be possibly going wrong here, it will help me in speeding it up further. Thanks, Tyson

5 6

recon-all error
by Linette Savage 17 Feb '17

17 Feb '17

Hello, New to freesurfer using Linux (successfully reconstructed several images on a mac) - can you help me determine how to correct the error in this attached attempt at a recon? Many thanks, Linette

2 2

Question regarding comparison image
by Dawn C. Matthews 17 Feb '17

17 Feb '17

In the image comparing the subfield segmentation for versions 5.3 and 6.0 found at https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields, the segmentation by version 6.0 does not capture a gray segment that 5.3 includes, located superior to the other regions. Was it omitted by 6.0 because it is part of a separate anatomical structure, not hippocampus? As a second question, in each case, does the totality of the colored subregions comprise what would be considered to be the total hippocampal volume (at least as represented in the slice shown)? Thanks very much for your time in answering.

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recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding
by Jared Saletin 17 Feb '17

17 Feb '17

Hi Freesurfer gurus: I recently installed 6.0.0 on MacOS 10.12 and recon-all is exiting with an error in mris_smooth. It looks like a library issue. A prior post had the same issue and indicated uninstalling the whole distribution and re-installing 6.0.0 fresh (as opposed to installing over 5.3). I receive the same error however (pasted below). Does anyone have any thoughts? Thanks! Jared > #@# Smooth1 rh Thu Feb 16 16:47:23 EST 2017 > /Users/jared/Desktop/fMRITest/test/scripts > \n mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix \n > Waiting for PID 11130 of (11130 11133) to complete... > /Applications/freesurfer/bin/reconbatchjobs: line 81: 11130 Abort trap: 6 exec $JOB >> $LOG 2>&1 > Waiting for PID 11133 of (11130 11133) to complete... > /Applications/freesurfer/bin/reconbatchjobs: line 81: 11133 Abort trap: 6 exec $JOB >> $LOG 2>&1 > > mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix > > setting seed for random number generator to 1234 > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address > Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > dyld: Symbol not found: ___emutls_get_address > Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > > mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix > > setting seed for random number generator to 1234 > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address > Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > dyld: Symbol not found: ___emutls_get_address > Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > PIDs (11130 11133) completed and logs appended. > Darwin Jareds-iMac.local 16.4.0 Darwin Kernel Version 16.4.0: Thu Dec 22 22:53:21 PST 2016; root:xnu-3789.41.3~3/RELEASE_X86_64 x86_64 > > recon-all -s test exited with ERRORS at Thu Feb 16 16:47:23 EST 2017 — Jared M. Saletin, PhD Assistant Professor of Psychiatry and Human Behavior Alpert Medical School of Brown University E.P. Bradley Sleep Research Lab 300 Duncan Drive Providence, RI 02906 Email: jared_saletin(a)brown.edu Phone: 401-421-9440 Fax: 401-453-3578

2 1

qdec significancy level
by Eva Wiedemann 17 Feb '17

17 Feb '17

Dear freesurfer-community, I want to compare cortical thickness in a group of Alzheimers patients's to healthy controls. Therefore I ran qdec setting the threshold to Min:1.3, Max:5 (assuming this would give me a significance level of p<=0,05). When I extract the cortical-thickness-data for the ROIs with "aparcstats2table" and perform two-sample-t-tests (assuming unequal variancies) on those, I can see highly significant (p<0,001) differences in many more ROIs, which don't show any significant differences on qdec. Does qdec use any corrections for multiple testing? which statistic test is qdec using? Why do the significancy level and the areas/ROIs showing significant differences differ between qdec and the extracted ROI-Data? I'm using freesurfer v.5.3.0 on Ubuntu 15.10. Thanks for your help in advance! Yours sincerely, Eva Wiedemann

1 0

FreeSurfer stable v.6 Installation
by Duy Nguyen 17 Feb '17

17 Feb '17

Dear FreeSurfer experts I would like to ask that whether or not I can install the package to the existing FS 5.3 that previously installed on our Linux system? Please forgive if it is an obvious question. Thanks *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme(a)gmail.com <duy.nguyenbme(a)gmail.com>*

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Extract volume, thickness, and surface area from all vertices in a cluster
by Shady Rahayel 16 Feb '17

16 Feb '17

Hi everybody, I compared 2 groups and found a cluster with difference in cortical volume. I want to have a mean value of cortical volume, thickness, and surface area for each subject for this cluster, that I can use for further statistical analysis. What do you recommend? I'm not looking for a value that would only be the one from the peak vertex (I've tried it with mri_segstats already). I'm rather looking for a volume, thickness and surface area value from EACH vertex from the cluster, so that I can have a mean value for each metric if I average them with a basic statistical tool. I searched the forum quite a bit and all the different replies are confusing me. Thank you very much Shady -- *Shady Rahayel* Étudiant au Ph.D. en neuropsychologie R/I Université du Québec à Montréal Centre d'Études Avancées en Médecine du Sommeil Hôpital du Sacré-Coeur de Montréal

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Re: [Freesurfer] Intensity Re-scaling Relative to Full Brain Atlas <Repost>
by Anderson Napolitano 16 Feb '17

16 Feb '17

I am so sorry about that Dr. Greve. The post I made earlier is reference from the following thread: On 02/16/2017 12:28 PM, Anderson Napolitano wrote: > > Thank you Dr. Greve. Just to clarify, the 'inputfile.nii.gz' file in > the command: > > fscalc inputfile.nii.gz div value -o outputfile.nii.gz > ,is the gtm.nii.gz file generated after the command: > mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg > gtmseg.mgz > --default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output > located at gtmpvc.output directory? If that's the case, fscalc will > not modify > gtm.stats.dat file corresponding to the image. Wouldn't that be > counter intuitive, > as gtm.stats.dat remains unchanged but we just normalized the image > using the > fscalc command? > Again, thank you Dr. Greve. I really appreciate all the help. > -Anderson >> There is not a flag to do this, but it should be fairly easy. There will >> be a file called aux/global.gmwmcsf.dat. This has the mean value average >> over all GM, WM, and CSF voxels (after PVC). You can use this to scale >> your data like >> fscalc inputfile.nii.gz div value -o outputfile.nii.gz >> You can also use the --scale option when running mri_vol2surf to apply a >> scaling factor when projecting on to the surface On 02/14/2017 02:04 PM, Anderson Napolitano wrote: >>> Hi Experts! >>>? >>> >>> Quick question: is it possible to re-scale intensities relative to the full >>> brain atlas? >>> Details: >>> Per step 3 of the following tutorial: >>> >>> https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer >>> >>> >>> I wanted to re-scale the the intensities relative to the full brain atlas. The >>> command: >>> >>> --no-rescale >>> >>> removes scaling relative to the Pons and the command: >>> >>> --rescale <Ids> >>> >>> rescales the intensities relative to the region determined by Ids. Would >>> listing all the regions on the --rescale command be the right approach to >>> rescale the intensities relative to the atlas? If so, how do I determine which >>> Ids is which? >>> >>> >>> Thank you in advance! >>> >>> >>> -Anderson >>> >>> >>> >>> >>> _______________________________________________ >>> 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 >> >>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/ >> >>_______________________________________________ >>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

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Re: [Freesurfer] Talairach Registration Error : recon-all -s
by Antonin Skoch 16 Feb '17

16 Feb '17

Dear Experts, according to the log, Vasudev is using version 5.3-HCP. Therefore I expect that he is running FreeSurfer inside HCP pipeline scripts. The problem is that the use of 6.0 version with HCP pipeline scripts is not currently recommended. see http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51416.html Antonin

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