Freesurfer

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30132 discussions

Registration error
by Harrigan, Timothy P. 24 Feb '20

24 Feb '20

External Email - Use Caution Hi, I'm trying to learn to use Freesurfer to see if I can use it for some academic work on TBI. I downloaded it to a spare laptop at home, and filled out the registration form, and I got a message that stated "Registration Error: Spammer. Go Away." How could I address this? Thanks Tim Timothy P. Harrigan ScD Research and Exploratory Development Division Johns Hopkins University Applied Physics Laboratory Phone: 240-228-5943 Cell/Text: 240-280-9444

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how to convert the registered file (.lta) into NIfTI format in PETsurfer
by Kate Marvel 24 Feb '20

24 Feb '20

External Email - Use Caution Hi All, How do you convert the registered file (.lta) into NIfTI format in PETsurfer. Thanks,

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skull stripping problem
by Marina Fernández 24 Feb '20

24 Feb '20

External Email - Use Caution Dear Freesurfeer experts, After running the recon-all, a part of the temporal lobe of one subject was removed. I used the watershed algorithm to be less agressive in the skull stripping step: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001 And the problem was solved in the brainmask.mgz volume because I can see the temporal lobe completely, but the surfaces are still displaced. In order to correct the surfaces I used the white matter edit tool but there is no change after correcting WM and running the recon-all -autorecon2-wm -autorecon3. I also used control points and but the following error was shown in the terminal when I run the recon-all -autorecon2-cp -autorecon3: recon-all -s sub_001 existed with errors I detected that there are very high values in the white matter of this part of the temporal lobe (even 132), maybe it has something to do. What can I do to solve the problem with this subject? Thank you very much in advance. Best regards, Marina.

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cluster size threshold
by Elisa Castaldi 24 Feb '20

24 Feb '20

External Email - Use Caution Dear experts, To perform a Monte Carlo based cluster correction, I have run the following line: mri_glmfit-sim --glmdir glmdir --mczsim 3 abs --cwp 0.05 --2spaces --a2009s I need to figure out which is the minimum number of voxels required for a cluster to be considered significant. In other words, which is the cluster *size* threshold in this case? Where can I find this information? Thanks Elisa

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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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