Freesurfer

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30080 discussions

Visualizing Volumetric Files on Surface
by Maedeh Khalilian 08 May '19

08 May '19

External Email - Use Caution Dear FreeSurfer experts; I have created some volumetric(.nii) files in FreeSurfer (the procedure is as following: lh/rh.aparc.annot> mri_divide_parcellation > mri_aparc2aseg > deleting subcortical and white matter regions in order to keep just cortical regions on GM). Now I wanna visualize my volumetric files on surface so that I myself can determine the color of each region. But I dunno how to do it exactly. I would be grateful if u could help me with that. Thanks in advance Best regards Maedeh,

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Re: [Freesurfer] Cortex reconstruction using MRI with contrast
by Dengyu Wang 08 May '19

08 May '19

External Email - Use Caution Hi Bruce, My previous email with the wm.mgz and orig.nofix files was held by the system because of the big size. So in this email I attached some pictures about the wm and orig.nofix visualized in Freeview: Hope to get your opinion. Thank you! Best, Dengyu > On May 8, 2019, at 11:01 AM, Dengyu Wang <wangdy1995(a)gmail.com> wrote: > > Hi Bruce, > Thank you for your remind and I will keep in mind in the future. > > Here are the wm.mgz, lh.orig.nofix and rh.orig.nofix > > <wm.mgz> > <lh.orig.nofix> > <rh.orig.nofix> > > I tried to open in Freeview but Freeview always collapsed. > > Best, > Dengyu > >> On May 8, 2019, at 10:45 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> >> Hi Dengyu >> >> I meant images of the brain. In general don't send us images of text - just send us the text so we can search and paste and such. In this case you have a huge defect that is probably caused by dura connecting to the wm. You need to look at the orig.nofix surfaces and the wm.mgz. You might need to make the skull stripping more aggressive and/or manually edit out some of the dura, but I can't tell without seeing the dataset. >> >> cheers >> Bruce >> On Wed, 8 May 2019, Dengyu Wang wrote: >> >>> External Email - Use Caution >>> Hi Bruce, >>> Thank you for your reply! And here is the detail: >>> >>> I use the command below to start the reconstruction: >>> >>> >>> >>> 366 defects are found in the process: >>> >>> >>> >>> And then says 281 defects to be corrected, and starts correcting the defect: >>> >>> >>> And then it gets stuck in correcting defect 46 and can’t move on: >>> >>> >>> We won’t have problem with t1 image without contrast, but in this special case we only have t1 with contrast. Do you have any ideas about this problem? Thank you! >>> >>> Best, >>> Dengyu >>> >>> >>> >>>> On May 7, 2019, at 4:37 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >>>> Hi Dengyu >>>> you need to tell us what went wrong. We have reconned lots of brains with contrast, although sometimes the skull stripping needs to be played with to get it to work >>>> cheers >>>> Bruce >>>> On Tue, 7 May 2019, Dengyu Wang wrote: >>>> >>>>> External Email - Use Caution >>>>> Hello FreeSurfer developers, >>>>> I am writing to ask about problem I met when reconstructing cortex from MRI with contrast? I had one subject that had only with contrast MRI images, and the recon-all can’t finish successfully. Is there any method or parameter setting that can solve the problem? Thank you! >>>>> Best, >>>>> Dengyu >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Freesurfer default git clone branch
by Bignamini Christopher 08 May '19

08 May '19

External Email - Use Caution Dear list members, I would have a question about the naming of Freesurfer branches: I cloned the repository in order to build the code on my system and the default branch is the dev one. Should I switch to master in order to work with a stable code version or the dev one is fine? Thank you very much in advance for your attention. Best regards Christopher Bignamini

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Cortex reconstruction using MRI with contrast
by Dengyu Wang 08 May '19

08 May '19

External Email - Use Caution Hello FreeSurfer developers, I am writing to ask about problem I met when reconstructing cortex from MRI with contrast? I had one subject that had only with contrast MRI images, and the recon-all can’t finish successfully. Is there any method or parameter setting that can solve the problem? Thank you! Best, Dengyu

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White surface area and cortical surface area
by Ting Li 08 May '19

08 May '19

External Email - Use Caution Dear Freesurfer Experts, I have a very simple question. The white surface area we extract from the ?h.aparc.stats is the same area we used in the mri_surf2surf by parameter area? or the mri_surf2surf is the pial surface area? I am looking forward to your response. Thanks a lot! Best regards, Ting

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Running multiple variables in mri_glmfit
by Erik Lindberg 08 May '19

08 May '19

External Email - Use Caution Dear Freesurfer experts, I am in the processing of running correlation with cortical thickness for almost 500 CSF variables. Thus I would like to use some sort of script. I previously used the common steps (mri_preproc, mri_glmfit and mri_glmfit-sim) but this procedure does not allow a .fsgd file with all the 500 CSF variables in it … correct? When running qdec many csf variables can be in the file … but then I cannot run it by script … right? So I wonder if there is a way to use one large file with the CSF data and then to make a script so that each variable is run iteratively until all is finished. Best case scenario I would also like to include snapshots from each correlation analysis. Is this possible to do? Thanks Olof Lindberg

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skullstripping outside freesurfer
by Eric Cunningham 07 May '19

07 May '19

External Email - Use Caution Dear Freesurfer Experts, I have recently processed some data with the following 2 steps: 1) Perform skullstripping outside freesurfer to generate a nifti file (mostly using AFNI). 2) Run that through freesurfer using the -noskullstrip flag. Comparing the results from this with just running freesurfer alone, I found that the eTIV was significantly smaller, and not terribly well correlated (R^2 of .65). When looking at cortical volume measurements, it is generally considered a good idea to correct for eTIV. How would you recommend doing so in this case? Freesurfer version 5.3. Thanks, -Eric

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funcroi-table-sess
by Nasiriavanaki, Zahra 07 May '19

07 May '19

Dear Freesurfer experts Hi I have a question about funcroi-table-sess, and I appreciate if you could please find a time to reply. Is there anyway that funcroi-sess-table can give out the activation values in each timepoint separately? Right now I can get the average of activation in each subject (in a specific region of interest and a specific contrast) by using the below commands, and I was wondering if I can get the values in each timepoint. funcroi-config -label ${lable}.label -roi ${subj}/${label_lh}.cfg -analysis loom.lh -force funcroi-sess -roi all_subjects/${subj}/${label}.cfg -s all_subjects/$subj -d . funcroi-table-sess -roi all_subjects/${subj}/${label}.cfg -s all_subjects/$subj -d . -o all_subjects/$subj/ROI_analysis/${label_lh}_${contrast}.txt -c $contrast -m cespct Thanks MOna

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Conjunction analysis on the results of task-based fMRI
by Zhi Li 07 May '19

07 May '19

External Email - Use Caution Dear Freesurfer experts, I would like to investigate the overlap between two contrasts with conjunction analysis. May I know how should I use mri_glmfit-sim to correct the combined sig.nii.gz of contrast A and contrast B? Another question is if I want to do conjunction analysis on the corrected p maps of both contrasts, which file should I use, 'perm.th30.pos.sig.cluster.nii.gz' or 'perm.th30.neg.sig.voxel.nii.gz'? Besides, what is the difference between the p value in 'perm.th30.pos.sig.cluster.nii.gz' and 'perm.th30.neg.sig.voxel.nii.gz'? I tried to visualize the 'perm.th30.neg.sig.voxel.nii.gz', the figure was a little weird that the significant part in this file seemed to the the boundary of the uncorrected 'sig.nii.gz', is that correct? I asked a similar question before, maybe the post has been lost that I did not get answers. I am still confusing on the forming of the file 'perm.th30.pos.sig.cluster.nii.gz'. If the value in each cluster of this file is CWP, how does this p value generates (the CWP within a cluster is the same, but zero outside clusters)? Any suggestions would be much appreciated. Thanks and best wishes, Lizhi

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dimensions swapped with head first-prone acquisition
by Caspar M. Schwiedrzik 07 May '19

07 May '19

External Email - Use Caution Hi! I have data acquired on a Siemens scanner with head first-prone. When I convert the dicom files to MGZ, left and right and superior and inferior, respectively, are swapped. The anterior-posterior dimension is ok. I am wondering what the correct way to correct this is? Following this entry in the wiki https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal, it seems that I can use mri_convert with --in_orientation for that, and the images indeed look correct when I do this. I am however wondering whether I have to do the conversion to COR and fix the RAS coordinates as well? I found a 2007 entry on the mailing list about that https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-October/006250.h…, but it does not specify how to proceed. Your advice would be appreciated! Thanks, Caspar

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