Freesurfer February 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
143 discussions

Re: [Freesurfer] surfreg function
by Marina Fernández 24 Feb '20

24 Feb '20

External Email - Use Caution Hi Doug, Thank you for your replay. I understood that if I did not specify "--surfreg my_avg_subject.sphere.reg" mri_preproc was going to use the original file ( sphere.reg), because in the help of mri_preproc it mentions this: --surfreg SurfReg : default is sphere.reg With this in mind, do you think it would not be necessary to specify it in mris_preproc? What is the difference between sphere.reg and my_avg_subject.sphere.reg? Best wishes, Marina

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GLM DOSS questions
by Ferraro, Pilar 24 Feb '20

24 Feb '20

External Email - Use Caution Dear Freesurfer experts, I’ve just completed a GLM analysis in Freesurfer and I’d like to be sure that all the steps I’ve performed are the right ones. My analysis is looking at age related changes in cortical thickness in one group of patients, after regressing out the effects of disease duration. I obviously assume an inverse relationship between age and cortical thickness so that older age would be associated with cortical thickness reductions in specific brain regions. To test this hypothesis with Freesurfer I’ve used a GLM DOSS design. I’ve generated a fsgd file with the first column being the list of patients, the second column the age of patients, and the third column the disease duration. Then I’ve run the mris_preproc command. Afterward, I’ve generated 2 contrast matrices (one for the left and one for the right hemisphere) with the following structure: 0 -1 0. 1 question. Is the contrast matrices structure I’ve chosen the most appropriate one for the hypothesis I’d like to test? Then, I’ve run the glm analysis using the mri_glmfit command. To visualize the results I’ve used the freeview -f command and set the overlay_threshold to 1,5 instead of 4, cause I was interested in looking at all results significant at p < 0.05. 2 question. Is the overlay_threshold I’ve used the correct one? Lastly, I was interested in looking at my results after Montecarlo correction, so I’ve run the simulation using the mri_glmfit-sim command. However, here I’ve changed few options: mri_glmfit-sim \ --glmdir lh.dur.glmdir \ --cache 4 neg \ (here I’ve changed to 1,5 since I was interested again at a P value < 0,05 and not < 0.0001 and I’ve changed the neg option with abs since I was interested in absolute values identified through the previously run analysis) --cwp 0.05\ --2spaces 3 question. Are the edits I made to the command correct? It is not perfectly clear to me which one should be the preferred sign for the analysis (neg, pos or abs?). In the end, in order to visualize the Montecarlo corrected results I’ve used again the Freeview -f command and again I’ve sent the overlay threshold to 1,5 since I was interested in all significant clusters at P < 0,05. 4 question. Again, this threshold is the correct one for my purpose? I have one last question concerning the Montecarlo simulation. Are there any cases in which you would suggest to do not use it since it would not be an appropriate correction? Sorry for the long email but I needed to report all the steps in order to get an answer. Many thanks for all the help you’ll be able to provide. Best, Pilar Ferraro

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Re: [Freesurfer] PetSurfer questions
by Soo-Jong Kim 22 Feb '20

22 Feb '20

External Email - Use Caution Thank you Dr.Greve. I applied to rbv.nii.gz volume to anatomical space. You said, bbpet2anat.lta. using mri_vol2vol but I tested. registration using bbpet2anat.lta was not correct on native T1 space. So I tested rbv2anat.lta for registration. that was okay. What is difference between SPM coregistration rbv onto orig.mgz and registration using rbv2anat.lta?? Best regards Soo

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Re: [Freesurfer] tksurfer
by fsbuild 22 Feb '20

22 Feb '20

External Email - Use Caution Hello Amar, You will probably need to install some software in Ubuntu in order to run freeview (and other commands in the  freesurfer distribution).  I would start with installing the list of packages  with the "sudo apt-get install" command for the packages listed in the Ubuntu section under freesurfer wiki page, https://surfer.nmr.mgh..harvard.edu/fswiki/BuildRequirements If the packages are already installed, the apt-get command should tell you there is nothing to do.  After installing those,  I would try running freevew. FYI, there is a more extensive list of packages needed to build and compile the freesurfer source code here starting at line 11, https://github.com/corticometrics/fs-docker/blob/20190925-update/build/Dock… but you should need to install those just to run freeview and the other commands. - R. On Feb 22, 2020, at 03:13, Amar Shukla <amar28071989(a)gmail.com> wrote:        External Email - Use Caution        Dear Support Team,I am starting the work in the field of capturing the anatomical features from the brain through free surfer, but still lot of issue i am facing through installing free surfer in in linux through VM ware or in windows 10 using ubuntu bash,So kindly guide me to start working , i spent day and night  i am not able to run. Please help me out ,with any doc or any installation guide.🙏🙏 please help meregardsAmar ShuklaPHD studentOn Sat, 22 Feb 2020, 00:18 Bruce Fischl, <fischl(a)nmr.mgh.harvard.edu> wrote:Hi Emalietksurfer and tkmedit have been deprecated for a long time.. Can you try using freeview instead?cheersBruceOn Fri, 21 Feb 2020, Emalie McMahon wrote:> >         External Email - Use Caution        > > Hello, > I get an error (see below) when opening tksurfer and tkmedit. Is there> anyway to resolve this? > > tksurfer s001 lh inflated> /Applications/freesurfer/tktools/tksurfer.bin: Bad CPU type in executable.> > Freesurfer Details: > freesurfer-i386-apple-darwin11.4.2-stable6-20170119> > > OS Details: > Computer: 2019 Macbook Pro> OS: macOS 10.15.2 Catalin> Processor: 2.4 GHz 8-Core Intel Core i9 > > Best, > Emalie McMahon> PhD Student> Johns Hopkins University> >_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Question regarding Qdec vs mri_glmfit
by 邓刊 22 Feb '20

22 Feb '20

External Email - Use Caution Dear Freesurfer support, we met some probelm when we investigate difference between two groups. We have two sets of data, one is the TLE group, the other is the extraTLE. We also has the variables: age,gender and neuropsychological test scores. We want to analyze the relationship between cortical thickness and neuropsychological test, controlling for age, gender and group. The contrast in the full DODS model in the mri_glmfit is 0 0 0 0 0.5 0.5 0 0, with the fsgd file being: GroupDescriptorFile 1 Title MyTitle MeasurementName thickness Class Class1_TLE Class Class3_extra_TLE Variables Age factor4 gender Input PT1_01 Class1_TLE 23 12 1 Input PT1_03 Class1_TLE 38 10.26 0 Input PT1_04 Class1_TLE 26 13 0 Input PT1_06 Class1_TLE 45 13 1 Input PT1_11 Class1_TLE 20 15 1 Input PT1_12 Class1_TLE 23 10.26 0 Input PT1_14 Class1_TLE 39 9 1 Input PT1_27 Class1_TLE 51 14 1 Input PT1_32 Class1_TLE 33 11 0 Input PT1_33 Class1_TLE 27 8 1 Input PT1_34 Class1_TLE 19 8 0 Preproc was done with: mris_preproc --fsgd patients_age_gender_Arithmetic.fsgd \ --cache-in thickness.fwhm15.fsaverage \ --target fsaverage \ --hemi rh \ --out rh_thickness_Arithmetic/rh.thickness.fwhm15_arithmetic.mgh GLM was done with: mri_glmfit --y rh_thickness_Arithmetic/rh.thickness.fwhm15_arithmetic.mgh \ --fsgd patients_age_gender_Arithmetic.fsgd dods \ --C difference_Arithmetic_all.mtx \ --surf fsaverage rh \ --glmdir rh_thickness_Arithmetic My questions are： (1)Are the command lines, fsgd file and the contrast matrix correct? (2)We have used qdec (DODS) to visualize the results, but I can't open the sig.mgh file. I dont know why? The terminal shows that : Reading /usr/local/freesurfer/tktools/tkUtils.tcl Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl ERROR: MRISread: file '/usr/local/freesurfer/subjects/Neuropsychology/rh_thickness_Arithmetic/difference_Arithmetic_all/F.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface! Invalid argument I dont know how to solve it. I very appreciate your help. Kind regards, Kan

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tksurfer
by Emalie McMahon 22 Feb '20

22 Feb '20

External Email - Use Caution Hello, I get an error (see below) when opening tksurfer and tkmedit. Is there anyway to resolve this? tksurfer s001 lh inflated /Applications/freesurfer/tktools/tksurfer.bin: Bad CPU type in executable. Freesurfer Details: freesurfer-i386-apple-darwin11.4.2-stable6-20170119 OS Details: Computer: 2019 Macbook Pro OS: macOS 10.15.2 Catalin Processor: 2.4 GHz 8-Core Intel Core i9 Best, Emalie McMahon PhD Student Johns Hopkins University

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Error in long_mris_slopes
by Guillaume Carey 21 Feb '20

21 Feb '20

External Email - Use Caution Hello everyone, I’m currently working on a longitudinal FreeSurfer pipeline in order to compare cortical thickness changes across the time. I’m using FreeSurfer version 6.0.0 (OS: Scientific Linux 7.3). I already processed the recon-all, -base and -long processing steps. Now I’m trying to run the “long_mris_slopes“ processing in order to prepare the data for a two stage model analyze. But there is an error. The command: long_mris_slopes --qdec ./qdec.dat --meas thickness --hemi lh --do-spc --do-label --time month --qcache fsaverage --sd $SUBJECTDIR At first everything seems to work well for the 1st subject and then: ================================================================== SUBJECT CBTPD-001/template_CBTPD-001 mapping label to QCache (…) Writing label file /data/guillaume/ParkAnx3/freesurfer/results/CBTPD-001/template_CBTPD-001/label/lh.long.cortex.fsaverage.label 167889 mri_label2label: Done Traceback (most recent call last): File "/opt/mumc/apps/freesurfer-6.0.0/bin/long_mris_slopes", line 868, in <module> dirname = tempfile.mkdtemp('',prefix,'') File "/usr/lib64/python2.7/tempfile.py", line 329, in mkdtemp _os.mkdir(file, 0700) OSError: [Errno 2] No such file or directory: './tmp-CBTPD-001/template_CBTPD-001_lh_thickness_wuK7ZI' It seems like the output “lh.long.cortex.fsaverage.label” has been created for this subject. But then there is a missing “tmp” folder. I haven’t find this error in the archives. Does anyone have an idea of how to fix it ? Best, Guillaume

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questions about batch running longitudinal data using long_submit_jobs on cluste
by Huang, Yiting 21 Feb '20

21 Feb '20

Hi there, I am trying to run some longitudinal data using freesurfer long_submit_jobs command on cluster. I have double checked my directory and files setup according to freesurfer longitudinal preprocessing wiki:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts. And it seems there is no problem with my setup. However, when I run the command it keeps sending me error as below: launchpad:yh917[21] long_submit_jobs --qdec long.qdec.table.dat --cdir $PWD/../ --cross --base --long --pause 5 --max 200 --queue max100 File "/usr/local/freesurfer/stable6_0_0/bin/long_submit_jobs", line 94 print "job submission failed, maybe unknown host "+hostname ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("job submission failed, maybe unknown host "+hostname)? I can't figure out the reasons. Any help please? Thanks, Yiting

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bias correction on 7T MEMPRAGE
by Barletta, Valeria 21 Feb '20

21 Feb '20

Dear Freesurfers, I am trying to apply the bias correction on the 7T MEMPRAGE through the unified segmentation algorithm on SPM12, as a primary step to do the submillimetric recon on Freesurfer, as you suggested here: https://surfer.nmr.mgh.harvard.edu/fswiki/HighFieldRecon For some reason, I cannot set the Bias FWHM to 18 on the SPM12 interface. Also, not sure how to use the 5D image that I obtain from the process. Have you ever done this before? Any tips? Thanks a lot, Vale

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how to perform No Partial Volume Correction for PET using PETSURFER
by Kate Marvel 20 Feb '20

20 Feb '20

External Email - Use Caution Dear All, I would like to perform no partial volume correction of PET using PETSURFER. The steps followed in doing this is shown below: gtmseg --s Patient_1 mri_concat Patient_1_pet.nii.gz --mean --o Patient_1_pet_tac_vol_mean.nii.gz mri_coreg --s Patient_1 --mov Patient_1_pet_tac_vol_mean.nii.gz --reg Patient_1_pet_registration.lta --threads 4 mri_gtmpvc --i Patient_1_pet.nii.gz --reg Patient_1_pet_registration.lta --no-tfe --psf 0 --seg gtmseg.mgz --o Patient_1_gtmpvc.output.psf6 I would like to know whether these steps suffices for a no partial volume correction. Thanks. -- kate

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Freesurfer February 2020