Re: [Freesurfer] Hippocampal subfield analysis did not run or produce right hemisphere outpus

External Email - Use Caution Hi Zola, What version of FreeSurfer was this? Can you please send us the log? Cheers Eugenio Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu

[Freesurfer] Hippocampal subfield analysis did not run or produce right hemisphere outpus

External Email - Use Caution Dear all I ran the hippocampal subfield analysis with this script: recon-all -s HP_0015 -hippocampal-subfields-T1, and this completed without errors. However, looking at outputs inside the mri directory, there is only the left hemisphere (3 of

Re: [Freesurfer] Fw: Yeo Atlas Network 3 segmentation FEF

External Email - Use Caution Hi Catherine, We have extracted the 7 and 17 networks into 51 and 114 regions respectively. See figures in https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering Unfortunately, we have only

Re: [Freesurfer] Trouble getting git-annex files

External Email - Use Caution Hello Rob, No, I mean the dmri_train binary that is part of Tracula. The main source file is ./freesurfer/trc/dmri_train.cxx. I don’t mind building the whole tree if necessary, but I haven’t been able to do so either. Do you know what the -r flag

[Freesurfer] freesurfer masks for fsl processed data

External Email - Use Caution Dear All, I ran fsl feat on my functional data and have all my data transformed into standard MNI space. However, I would like to use freesurfer generated white matter parcellation (wmparc.mgz) to extract white matter signals from my MNI space

Re: [Freesurfer] Trouble getting git-annex files

Hello Ruy, Do you mean the mri_train binary that gets built under ./freesurfer/mri_train ? (I see a ./freesurfer/dmri_poistats, ./freesurfer/dmri_tensroreig but not a ./freesurfer/dmri_train). Things are not necessarily setup so you can cd to ./freesurfer/ and just build what is there in

Re: [Freesurfer] combinesurfs problem: shifts and rotates

Does it work if you don't save it as an stl file? On 05/02/2018 06:39 AM, Klink-3, N.E.C. van wrote: > > > Dear all, > > I am struggling with coverting and combining pial surfaces back to > native space. My result is 90 degrees rotated, and shifted from the > original MRI. > > The initial

Re: [Freesurfer] visualizing seeds on surface

If you know the vertex number, then you can do something like mri_volsynth --template $SUBJECTS_DIR/subject/surf/lh.thickness --pdf delta --delta-crsf vertexno 0 0 0 --o delta.mgz mris_fwhm --smooth-only --fwhm 5 --i delta.mgz --subject subject --hemi lh --o delta.sm05.mgz mri_binarize --i

Re: [Freesurfer] visualizing seeds on surface

Hi Doug, They are in MNI but I can find out their vertex numbers if that would be easier. Thanks! Hamdi From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent:

Re: [Freesurfer] freesurfer selxavg3-sess error

oops, sorry. Looks like it is having a problem loading your paradigm file. Check that. If the error does not pop out to you then send it to me. On 05/02/2018 10:06 AM, Francesca Strappini wrote: > Hi, sorry, maybe my last email got lost. Is there anything I can try > to fix this problem with

Re: [Freesurfer] fMRI timecourse plot

No, that is just the raw time course. Are you trying to do an FIR model? On 05/02/2018 03:54 PM, Sarah Cole wrote: > > > Hi Doug, > > In the FSFAST tutorials, I keep seeing the attached slide. > I can tell this is a simple block design experiment. However, I am not > sure how the bottom left

Re: [Freesurfer] visualizing seeds on surface

What coordinate system are the seed coordinates in? Do you know the vertex number on the surface? On 05/02/2018 03:13 PM, Eryilmaz, H. Hamdi wrote: > > Dear freeview experts, > > Is it possible to display multiple seeds (i.e., as a small circle) on > freeview surface view by specifying their

Re: [Freesurfer] Trouble getting git-annex files

External Email - Use Caution Hello, I need help recompiling dmri_train for Mac. It seems like the instructions in the Mac Developer’s don’t work. When I cd to the trc subdirectory and run make, I am told there is nothing to do. I tried editing the Makefile, adding bin_PROGRAMS

[Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

External Email - Use Caution Hi. I am just getting my feet wet with running my subjects through the Freesurfer processing stream, so the following question night be a bit trivial (I hope): I have run qvlSegmentHippocampal subfields on one of my subjects, and it completed just

Re: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions

External Email - Use Caution Anastasia, Thank you for the input. Jim "The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the

Re: [Freesurfer] Difference between freesurfer home folders

I don't know. It looks like FS was installed twice into two separate directories. I assume from the names that they are both verrion 6, but I can't say for sure. On 05/02/2018 03:39 PM, Hurtado, Aura Maria wrote: > Hi all, > > I’m digging into data that was reconned a while ago. I see in the

Re: [Freesurfer] mri_vol2surf warning

And what is the voxel resolution of the input to mri_vol2surf? On 05/02/2018 03:35 PM, Rachel Bencic wrote: > > > Hello, > > The voxel resolution of the unwarped mov volume used in bbregister was: > > voxel sizes: 3.75, 3.75, 5.00 > > So the reported values in the warning appear

[Freesurfer] Difference between freesurfer home folders

Hi all, I’m digging into data that was reconned a while ago. I see in the recon-all.done files and some say: CMDPATH /usr/local/freesurfer/stable6/bin/recon-all and others say: CMDPATH /usr/local/freesurfer/stable6_0_0/bin/recon-all Is there a difference between the recon-all commands in the

Re: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions

You should be OK. After running the preprocessing, you can look at the structural segmentation that's been mapped to diffusion space (dlabel/diff/aparc+aseg.bbr.nii.gz) on the FA map (dmri/dtifit_FA.nii.gz). From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions

External Email - Use Caution The MR sessions were a few weeks apart on 9-10 year olds. How would I go about confirming the registration between the diffusion and structural data across sessions? Jim "The materials in this email are private and may contain Protected Health

[Freesurfer] visualizing seeds on surface

Dear freeview experts, Is it possible to display multiple seeds (i.e., as a small circle) on freeview surface view by specifying their coordinates? If there is no such feature, could you suggest an alternative way to visualize seeds? Thanks in advance! Best, Hamdi

Re: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions

Yes, you can. The only thing that TRACULA uses from the structural is the aparc+aseg, and specifically the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg. It's safe to assume that those positions will not have changed

[Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions

External Email - Use Caution We have acquired data on a few kids and have generated nice surfaces, however, the diffusion data we acquired (102 directions and AP/PA distortion maps) were suspect due to motion and results from Tracula were not ideal. We have since brought these

Re: [Freesurfer] Starting with Neuroimaging

there are also videos of the class lectures on the wiki On 05/02/2018 12:14 PM, Bruce Fischl wrote: > Hi Lan > > we have tutorials on our wiki with associated data that you could try > going through > > cheers > Bruce > On Wed, 2 May 2018, Lan Naoyuki wrote: > >> >> External Email - Use

Re: [Freesurfer] Differences in aseg.stats automatic results

External Email - Use Caution Thank you very much. I´ll check that!. On Wed, May 2, 2018 at 3:16 PM Douglas N. Greve wrote: > You are using two different versions of mri_segstats (probably two > different versions of FS) and getting different results.

Re: [Freesurfer] mri_vol2surf warning

When you ran bbregister, what was the voxel resolution of the mov volume? On 05/02/2018 01:28 PM, Rachel Bencic wrote: > > > Hello FreeSurfer Developers, > > I'm attempting to resample beta weights generated from AFNI’s > 3dDeconvolve command to individual subjects’ cortical surfaces. Prior >

Re: [Freesurfer] Differences in aseg.stats automatic results

You are using two different versions of mri_segstats (probably two different versions of FS) and  getting different results. Why not just use one version? On 05/02/2018 01:24 PM, Fernanda Hansen P. de Moraes wrote: > > > Good afternoon, > > I've got two types of aseg.stats results from the

Re: [Freesurfer] problem using mri_vol2label for subcortical regions

mri_surfcluster only works for surfaces (that's what the "surf" in the name means). If you want the centroid of a volume ROI use https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids On 05/02/2018 12:08 PM, Lucia Billeci wrote: > > > Dear Bruce, > > the ROI appears correct in

Re: [Freesurfer] Starting with Neuroimaging

External Email - Use Caution Hi Fernanda and Bruce, Thank you for your prompt replies! I will look into them. Best, Lan On Wed, May 2, 2018 at 11:14 AM, Bruce Fischl wrote: > Hi Lan > > we have tutorials on our wiki with associated data that you

[Freesurfer] kvlGEMSMatlab error: search direction is not a descent direction

External Email - Use Caution Hello FreeSurfer Developers, > > I'm attempting to run longitudinal segmentation of hippocampal subfields by > using the development version of FreeSurfer, but for some of my subjects I get > the following error: > > *** > Global

[Freesurfer] mri_vol2surf warning

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to resample beta weights generated from AFNI’s 3dDeconvolve command to individual subjects’ cortical surfaces. Prior to running 3dDeconvolve, I ran bbregister to coregister subjects’ (unwarped) functional

[Freesurfer] Differences in aseg.stats automatic results

External Email - Use Caution Good afternoon, I've got two types of aseg.stats results from the file automatically created from the regular script (recon-all -all). I am especially interested in the SupraTentorialVolNotVent. Here goes two examples:

Re: [Freesurfer] Starting with Neuroimaging

Hi Lan we have tutorials on our wiki with associated data that you could try going through cheers Bruce On Wed, 2 May 2018, Lan Naoyuki wrote: External Email - Use Caution Hello Freesurfer experts, I am a junior in Computer Science, and am planning to join a neuroimaging

Re: [Freesurfer] problem using mri_vol2label for subcortical regions

External Email - Use Caution Dear Bruce, the ROI appears correct in freeview. However I have a problem in the following step, i.e. obtain the centroid of the ROi. I used the following command: mri_surfcluster --in /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness

Re: [Freesurfer] Starting with Neuroimaging

External Email - Use Caution HI! The FreeSurfer Tutorials (http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials) give a good overview of how FreeSurfer works and each step of the analysis. Good luck and welcome! Fernanda On Wed, May 2, 2018 at 12:09 PM Lan Naoyuki

[Freesurfer] Starting with Neuroimaging

External Email - Use Caution Hello Freesurfer experts, I am a junior in Computer Science, and am planning to join a neuroimaging lab in the summer. As far as I know, one of the projects that the lab is interested in is structural MRI analyses of bovine brains, and they would like

Re: [Freesurfer] problem using mri_vol2label for subcortical regions

Hi Lucia the first column being -1 means that it is not mapped to the surface, so is correct in your (subcortical) case. Try loading the label as an ROI in freeview and see if it is correct cheers Bruce On Wed, 2 May 2018, Lucia Billeci wrote: External Email - Use Caution

[Freesurfer] Fw: Query regarding creation of atlas directly from probabilistic information

External Email - Use Caution Dear Everyone, A kind reminder. I'm unable to look beyond this step and am really looking for some help. I would like to know if we can use the probabilistic information directly on mri_train Thank you, Kind regards Mageshwar Selvakumar, M.Sc

Re: [Freesurfer] problem using mri_vol2label for subcortical regions

External Email - Use Caution Dear Brouce, thanks again. I would like exactly how to set mri_vol2label for subcortical regions as the way I used give me all the values of the first column equal to -1. This is a problem when I want to obtain obtain the centroid of the ROI using

Re: [Freesurfer] freesurfer selxavg3-sess error

External Email - Use Caution Hi, sorry, maybe my last email got lost. Is there anything I can try to fix this problem with selxavg3-sess? Thanks! Best Francesca 2018-04-24 20:35 GMT+03:00 Francesca Strappini : > Thank you for the reply! > I

Re: [Freesurfer] aseg labels in nii | FreeSurfer to other software

If you just need the aseg in nii.gz format, then you can mri_convert aseg.mgz aseg.nii.gz If you need a particular seg in its own file, then you can mri_binarize --i aseg.mgz --match 17 --o left-hippo.nii.gz where 17 is from $FREESURFER_HOME/FreeSurferColorLUT.txt On 5/2/18 5:47 AM, Otília

Re: [Freesurfer] orig.mgz versus T1.mgz

The orig.mgz is closer to the raw data than T1.mgz, but it will be different in a number of ways. First, it will be 256^3, 1mm voxel size regardless of the dimensions of the raw data. Second, it will be 8 bits (0-255) with some rescaling. On 5/2/18 7:43 AM, C.P.E. Rollins wrote: >

Re: [Freesurfer] orig.mgz versus T1.mgz

External Email - Use Caution Just to clarify, by that I mean would the NIFTI converted from orig.mgz (with mri_convert) be different than the NIFTI produced by dcm2niix from the raw DICOMs? Thanks, Colleen Original Message Subject: orig.mgz versus T1.mgz

[Freesurfer] Two year postdoc in Cambridge UK

External Email - Use Caution Dear Colleagues, I would like to draw your attention to a postdoc vacancy in Cambridge on the MQ funded HOPES

[Freesurfer] aseg labels in nii | FreeSurfer to other software

External Email - Use Caution Hi to all FS users! Sorry in advance if I'm _cross-posting_ but after searching and trying some stuff I still can't figure out how to do this. After all the processing in FS I would like to evaluate the labels (from each participant) in other

[Freesurfer] orig.mgz versus T1.mgz

External Email - Use Caution Thanks Bruce. Will the orig.mgz file be different from the raw data in any significant way? Thanks again, Colleen Original Message Subject: orig.mgz versus T1.mgz Date: 2018-04-30 11:54 From: "C.P.E. Rollins" To:

[Freesurfer] Mapping left to right for fsaverage 5 (ico5)

External Email - Use Caution Dear all, I have a question about left-right sphere based co-registration. I have a scalar quantity defined on the fsaverage5 ico5 surfaces and I would like to map left to right hemisphere. I’ve computed left_right registered spheres by running