Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Version Beta 7.0
by Victor Montal Blancafort 24 Feb '20

24 Feb '20

External Email - Use Caution Freesurfer developers, I have seen from the download webpage, that there is already a v7.0 beta version. Since we were planing to re-run a lot of individuals 1000+ with Freesurfer6, I was wondering if you could provide timings regarding the release of stabe 7.0. Also, could you briefly explain the main changes in this version? We are mainly interested on cortical thickness analysis, so... there will be big differences in the recon-all pipeline? Thank you in advance! V.

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Creating the pial surface of the cerebellum: how to let the mris_make_surfaces to push the pial surface to the boundary
by CiRong Liu 24 Feb '20

24 Feb '20

External Email - Use Caution Dear experts of the freesurfer, I was trying to create the white matter and pial surfaces of the cerebellum of the marmoset, based on ultra-high (80um) resolution ex-vivo images. I manually segment the cerebellum into the white matter and the gray matter and change the header information to 1mm. Based on the manual segmented files, I created white matter surfaces (rh.orig). I tried to use the mris_make_surfaces to expand the white matter to create the matched pial surface. However, the *mris_make_surfaces* failed to push the surface enough. See the attached files and screenshots. I tried smoothing the segmentation, enhancing the contrasts, and tested different expert option (for example: -max_csf 0.1 -min_gray_at_csf_border 1) This was this best I got, but still cannot get an optimal result (not pushed enough): *mris_mask_surfaces -max_csf 0.1 -min_gray_at_csf_border 1 -orig_wm orig -orig_pial orig -noaseg -noaparc -T1 ceb_sm marmosetceb rh * Since I have already manually segmented the cerebellum, *is there a way to force the mris_make_surfaces to expand to the boundary of the image?* The files can be download to replicate what I did: https://pitt.box.com/s/6269a9mnwbs6zi0azn08dn55u47yfa7i Thank you very much! Best Regards, CiRong Liu

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Optseq2 help needed
by Gergely Darnai 24 Feb '20

24 Feb '20

External Email - Use Caution Dear Developers, I am planning to run PVT (psychomotor vigilance task) in fMRI using event related design. This is an extremely simple reaction time task: participant has to respond to the appeared geometric shape as quickly as possible. The key feature of this paradigm is that we will have fluctuating and quite rapid event presentation times (ranging between 300 and 500 msec). Another important information is that we will use FSL FEAT for the evaluation. We decided to use opseq2 to optimize the design with the following parameters: optseq2 --ntp 150 --tr 2 --psdwin 0 20 --ev evt1 1 45 --nkeep 3 --o exp --nsearch 10000 --tnullmin 3 --tnullmax 11 --repvar 10 Although with this design I get quite satisfying efficiency and VRF scores I do not understand that if I decrease dPSD why does it have significant negative effect on efficiency and VRF. Could you explain this? If I understand well, this is the only option to shift the onset of the event from the scanning points, and I would assume that if there is fluctuation in time between scanning points and stimuli presentation, it would help to "catch" the hemodynamic response easier (if the stimulus onset always goes together with the scans, we can always catch the same timepoints of the HRF). Did I misunderstand something? If I use FSL that is based on HRF estimation (and not on FIR), do these parameters (dPSD) and scores (efficiency & VRF) have meaning and function at all? My last question is related to event duration. Although I have fluctuating and short events, as you can see I chose 1 sec (because it has to be the integer multiple of the dPSD). Is it problematic? Thank you for your suggestions, Gergely ----------------------------------------- Gergely Darnai PhD Department of Behavioural Sciences Medical School, University of Pécs Phone: +36/72/536-256 Fax: +36/72/536-257 H-7624 Szigeti u. 12, Pécs, Hungary

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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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