Re: [Freesurfer] Volume (WM Parcellation) of RightCerebralCortex--Freesurfer 6.0

External Email - Use Caution Thanks for your reply! You mean LeftCerebralCortex is actually lhCortex in aseg.stats, right? Best Regards, An Lijun Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> 于2019年11月19日周二 上午2:20写道： You can find it in aseg.stats under # Measure

Re: [Freesurfer] 4D multi-frame parcellation

it's not delicate - it's just confusing for us when you use it as it refers to a specific dataset cheers Bruce On Mon, 18 Nov 2019, An wrote: External Email - Use Caution Sorry for the confusion, I don't know it has a delicated meaning. I just followed the steps on the

Re: [Freesurfer] 4D multi-frame parcellation

External Email - Use Caution Sorry for the confusion, I don't know it has a delicated meaning. I just followed the steps on the freesurfer download and install webpage to install the software and then ran the recon-all command. I will try to avoid this kind of issues in the

Re: [Freesurfer] 4D multi-frame parcellation

why did you call it bert? It just makes things confusing On 11/18/19 2:53 PM, An wrote: > > External Email - Use Caution > > Here is my recon-all command line: > recon-all -i ana_Vol.nii -s bert -all > Many thanks. > > Best, > An > > > Greve, Douglas N.,Ph.D.

Re: [Freesurfer] use of .m3z transform output from mri_cvs_register

External Email - Use Caution Hi, I had mistakenly used the raw moving image in the mri_convert command. It should have been the norm.mgz from the moving subject. The output image from the mri_convert command now perfectly overlaps with the output from mri_cvs_register. Thanks,

Re: [Freesurfer] 4D multi-frame parcellation

External Email - Use Caution Here is my recon-all command line: recon-all -i ana_Vol.nii -s bert -all Many thanks. Best, An Greve, Douglas N.,Ph.D. 于2019年11月18日周一 下午2:33写道： > What was your original recon-all command? > > On 11/18/19 1:48 PM, An wrote: > > > >

Re: [Freesurfer] 4D multi-frame parcellation

What was your original recon-all command? On 11/18/19 1:48 PM, An wrote: > > External Email - Use Caution > > I want to map the intensities of the volumes on its corresponding > surface in order to get the functional values on each vertex in each > frame. I ran recon-all for the

Re: [Freesurfer] (no subject)

It gets the subcortical from apas+head.mgz which gets created along the way by xcerebralseg. You can create your own with xcerebralseg by specifying your volume as the mergevol. I think this will work, but I'm not sure. I'm assuming you've used the GCA to create your own subcortical seg for

Re: [Freesurfer] 4D multi-frame parcellation

External Email - Use Caution I want to map the intensities of the volumes on its corresponding surface in order to get the functional values on each vertex in each frame. I ran recon-all for the anatomical volume and saved all outputs(mri,labels,surf and etc.) in the bert folder.

Re: [Freesurfer] Brain lobules pooling- request

sorry, it is not clear to me what is going wrong here. Did the mri_annotation2label command fail? or mris_anatomical_stats command? On 11/17/19 9:55 PM, Samson Nivins wrote: > > External Email - Use Caution > > Hi FreeSurfer Team, > >   I am interested in individual lobular volume

Re: [Freesurfer] Question about the input for longitudinal processing pipeline

Do all images and time points have contrast? If some do and some don't, then I don't think you can properly do the analysis? On 11/15/19 10:06 AM, Darko Komnenić wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > I wanted to run the Freesurfer's longitudinal

Re: [Freesurfer] Cortical thickness values on a vertex base level

The sig file On 11/15/19 9:16 AM, Aicha Dijkshoorn wrote: > > External Email - Use Caution > > Thank you so much for your repsonse. > Could you maybe please tell us which input file we should use? > > Best wishes, > AIcha >

Re: [Freesurfer] Questions for PetSurfer

On 11/15/19 4:19 AM, Soo-Jong Kim wrote: > > External Email - Use Caution > > Dear FreeSurfer experts, > > I am a student in neuroimaging using FreeSurfer. > I have some questions and I don't know where to send questions. > That's why I found this mail and writing. > > I've studied

Re: [Freesurfer] Multiple comparisons

My preferred method is to use permutation https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm On 11/14/19 12:29 PM, Juan Rivas wrote: > > External Email - Use Caution > > I would like to know how the correction is made for multiple > comparisons in the

Re: [Freesurfer] 4D multi-frame parcellation

I don't understand what you are trying to do. I'm very confused by your mentioning of bert. What does bert have to do with any of your data? On 11/14/19 10:47 AM, An wrote: > > External Email - Use Caution > > Oops sorry for the mistakenly reply. I will pay more attention in the >

Re: [Freesurfer] Fw: surface group analysis with qdec

The problem is that all of your class=0 subjects have a 0 duration meaning that you cannot compute a duration slope for this class. In this special case, you can run a different-offset, same-slope analysis with --fsgd dur.fsgd doss Change your contrast matrix to 1 -1 0 On 11/14/19 9:47 AM,

Re: [Freesurfer] Question about design matrix for surface group analysis

You have 4 classes and 2 variables, so you will have 4*(2+1)=12 regressors: MTLE MExTLE FTLE FExTLE MTLEage MExTLEage FTLEage FExTLEage MTLEneuro MExTLEneuro FTLEneuro FExTLEneuro You are interested in the diff between TLE and xTLE on the neuro score regressing out the effects of gender and

Re: [Freesurfer] Volume (WM Parcellation) of RightCerebralCortex--Freesurfer 6.0

You can find it in aseg.stats under # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 272816.537999, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 260016.082731, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter

Re: [Freesurfer] Spatial smoothing for cortical folding measures

Usually not for LGI. People usually don't use curv or sulc in group studies, so the question does not usually come up. For thickness, we usually use 5-10mm On 11/13/19 9:49 PM, huyang wrote: > > External Email - Use Caution > > Dear FS experts, > > Is it necessary to do spatial

Re: [Freesurfer] Processor speed/cores vs cache size

It is pretty complex. If you're only running one job at a time, then faster processor is better On 11/13/19 3:00 PM, Pradyumna Bharadwaj wrote: > > External Email - Use Caution > > Hello, > > For running recon-all or tracula on a local workstation, is it > recommended to go for a higher

Re: [Freesurfer] Fwd: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm

You did not tell recon-all to do anything:) Try adding -all to your command line On 11/13/19 2:10 PM, Dalton Bermudez wrote: > > External Email - Use Caution > > > > -- Forwarded message - > From: *Dalton Bermudez* > > Date: Wed, Nov 13,

Re: [Freesurfer] HBT hippocampal segmentation

Forwarding Jean’s response: Hi Daniel, We used specific anatomical landmarks, visually inspecting the hippocampal head and body in an anterior-posterior direction. Once the uncus (the medial most region in the hippocampus) ends posteriorly, it is considered hippocampal body. The hippocampal body

Re: [Freesurfer] Fwd: Regarding Issue in reading binary files inside DICOM Directory

External Email - Use Caution We use the dcm2nii (or dcm2niix in the latest Linux version) from the MRICron software [1] to convert DICOMs to NIFTI format. Install it and run like: cd dir/with/dicoms /path/to/installed/dcm2nii . Note the dot (".") at the end of the command,