Freesurfer November 2017

freesurfer@nmr.mgh.harvard.edu

110 participants
198 discussions

Registration
by N Saf 08 Nov '17

08 Nov '17

Dear Experts, In the volume-based stream, if I'm right the FreeSurfer does two registration with MNI305 ,one affine and one nonlinear , is it possible to perform the nonlinear registration somewhere else and then use the result in FreeSurfer and run the rest of the analysis ? thank's alot for your great support. BRG, Nazanin

2 3

Qdec result
by hiroki.sato＠med.tohoku.ac.jp 07 Nov '17

07 Nov '17

Dear experts I'm using Qdec. I want to check regions where age and thickness are correlated, and regions where the thickness-age correlation differ between genotype(Hetero or WT). When I choose "genotype(Hetero or WT)" as Fixed factors and "age" as Continuous variables, I can choice the results "Does the correlation between thickness and age, accounding for genotype, differ from zero" and "Does the thickness-age correlation differ between Hetero and WT?". I have two questions. Is "Does the correlation between thickness and age, accounding for genotype, differ from zero" equal to the results of "Does the correlation between thickness and age differ from zero" that I choose only "age" as Continuous variables? I don't know the meaning of "accounding for genotype" but these two results are almost same. Does just a little different results come from the difference of Degrees Of Freedom? Thank you in advance. Best, Hiroki

2 1

missing register.dof6.dat
by Guy Avraham 07 Nov '17

07 Nov '17

Hello Freesurfer developers, I was running FSFAST preprocessing: preproc-sess -s [subject] -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 0 -per-run The process finished without errors. However, the register.dof6.dat is missing from the subject's folder. I could not find any error in the register.dof6.dat.log file (see attached). - Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c - OS: Ubuntu 16.04 LTS - recon-all.log file is also attached. Thanks! Guy

2 1

cut-off clusters size
by stdp82＠virgilio.it 07 Nov '17

07 Nov '17

Hi, I wonder if there is a consensus to thershold the size of clusters obtained by FS-FAST after FDR correction?To cut-off clusters size>10-15 mm2 should be good? or do you advise more than? ThanksStefano

2 1

mask volume calculation
by Ehsan Tadayon 07 Nov '17

07 Nov '17

Hello FS experts, I'm trying to get the volume of a binary mask on orig.mgz. I know that FS uses a more sophisitcated approach than simply counting the number of voxels within the mask and I'd like to apply the same approach. Is there any way to get the volume for a defined mask with the same approach that FS computes the volumes for aseg.mgz? thanks. Ehsan ‌

5 4

mris_preproc srcsurfreg Freesurfer 6.0
by M del Mar Velasco 07 Nov '17

07 Nov '17

Dear FreeSurfer experts, I am using mris_preproc command with following options: mris_preproc --s s_001 --s s_002 --s s_003 --target my_subject_average --hemi lh --meas my_input_surf.mgh --out /my_output_path/output_file I observe mris_preproc uses mri_surf2surf. My question is related to Freesurfer version. Using FreeSurfer 5.3, mri_surf2surf takes sphere.reg as srcsurfreg, while with Freesurfer 6 script mri_surf2surf has changed. It takes my_subject_average.sphere.reg (target of mris_preproc) as srcsurfreg. I get an error because my_subject_average.sphere.reg file doesn't exist inside s_001 folder. Why Freesurfer 6 changes srcsurfreg to $target.sphere.reg? What can I do in order to be coherent with my script which was designed using Freesurfer 5.3? Thanks in advance, M del Mar

2 1

mri_cvs_register: how to read/import .m3z warp file
by Stefano Zappalà 06 Nov '17

06 Nov '17

Dear FreeSurfer Developers, I am trying to visualize and modify the output warp field (in .m3z) of a mri_cv_registration call aimed at aligning a T1w scan to the MNI space. I was wondering how file format .m3z is organized, in order to read it with, for example, matlab. Or if there are simpler file format to convert the warp field to. No information about it seems to be reported in the website. Moreover, I've searched the list and a similar question was not answered. I was wondering if you have some suggestions in reading the output warp field of mri_cvs_register. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: ubuntu 16.04 LTS Many thanks, Stefano.

4 5

computing euler number error
by Sidwell, Amanda Burns 06 Nov '17

06 Nov '17

Hello, I ran a recon-all that exited with errors. I have attached the recon-all log. It seems to have stopped in the middle of Aseg stats. Can you help me with what commands to use to pick up where the recon left off? Thanks! Amanda

2 1

License issue
by Danny Deng 06 Nov '17

06 Nov '17

Dear FDs, According to the instructions, I have cut the 4 lines between the “CUT HERE”, copy and past the 4 lines into my license.txt file in the home directory to freesurfer folder as follow: ------------------------------------------------------------------------------------------------------- PART C. MISCELLANEOUS This Agreement shall be governed by and construed in accordance with the laws of The Commonwealth of Massachusetts without regard to principles of conflicts of law. This Agreement shall supercede and replace any license terms that you may have agreed to previously with respect to FreeSurfer. dannytang023(a)gmail.com 33367 *CL6BxmQcdv6k FScW2..sWlD9c -------------------------------------------------------------------------------------------------------- However,when I tried to test my installation using the sample-001, it shows the error message as follow: Xues-MacBook-Air:~ DannyDeng$ cp $FREESURFER_HOME/subjects/sample-001.mgz usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... target_directory Xues-MacBook-Air:~ DannyDeng$ mri_Convert sample-001.mgz sample-001.nii.gz mri_convert.bin sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /Applications/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- Xues-MacBook-Air:~ DannyDeng$ Please help. thanks However Best Regards, Danny Deng

1 0

Helping with convert tool
by Rosalia Dacosta Aguayo 05 Nov '17

05 Nov '17

Dear FreeSurfer list, My name is Rosalia and this is the first time I post an email on your list. I have never run FreeSurfer before and I have a doubt regarding the converting process. For every T1 folder, I have 192.ima files. I do not know how to pass from this point to .mgz. It seems that in the tutorial you are speaking about converting one .dcm file to .mgz file. In my case, I have 192 .ima files and I do not know how to pass them to one .dcm file and then to .mgz file. Even, I am not sure if I could work with .nii.gz files instead of .mgz because I know that my .nii.gz files are well oriented but I do not know if my .mgz files will have any orienting problem. I would be more than grateful if you could kindly help me with this question. Kind regards, Rosalia

2 1

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Freesurfer November 2017