Re: [Freesurfer] segmentation error

External Email - Use Caution Hi there, Just want to check if you get the recon-all files that I sent for an entire subject?! I am also wondering if the problem with the segmentation can be related to the small size of aged Portuguese brains considering the expected size based for

Re: [Freesurfer] Special image protocol

Hi Mustafa FreeSurfer should work fine with many image protocols. If you have the freedom to choose one, Andre van der Kouwe (ccd) can point you at the sequence he developed for Siemens. If you are using a different scanner give us the details and we can recommend something cheers Bruce On T

[Freesurfer] White matter volume from aseg

Hello, I am trying to extract the white matter volume based off the aseg.stats. I noticed the text includes "total cortical white matter volume" and I was wondering if that is the same as overall white matter volume in the brain? Thank you, Ambica Mehndiratta Clinical Research Coordinator Mass

Re: [Freesurfer] Special image protocol

I highly recommend the multiecho mprage at about 1mm. On 2/21/19 10:30 AM, Bruce Fischl wrote: > Hi Mustafa > > FreeSurfer should work fine with many image protocols. If you have the > freedom to choose one, Andre van der Kouwe (ccd) can point you at the > sequence he developed for Siemens. If you

Re: [Freesurfer] White matter volume from aseg

It is cerebral white matter, so it excludes brainstem and cerebellar white On 2/21/19 11:14 AM, Mehndiratta, Ambica wrote: > Hello, > > I am trying to extract the white matter volume based off the > aseg.stats. I noticed the text includes "total cortical white matter > volume" and I was wonderin

Re: [Freesurfer] mris_preproc error: dimension mismatch

If you have a volume and a registration file, you can run mris_preproc with the --iv option. Eg, something like mris_preproc --fsgd abc.fsgd --target fsaverage --hemi lh \ * --out abc-lh-vol.mgh --iv abc01-func/bold/main/nvr/ces.bhdr abc01-func/bold/register.lta --iv abc02-func/bold/main/n

Re: [Freesurfer] Fw: clusters annotation file in surface - ERROR

what happens if you load it into freeview instead of tksurfer? How did you create lh.surf_combined-magn_CL_fwhm1.mgh ? Does it look ok on the surface? Are the values integers? On 2/20/19 12:56 PM, Barletta, Valeria wrote: > Thank you Doug, > As you suggested, I tried to use that command > (mris_

Re: [Freesurfer] mri_convert

you mean you want the acquisition times to do kinetic modeling? I don't have anything to do that. Also, you should check to see whether your PET has intensity scaling imbedded in the dicom as the v6 mri_convert does not handle this properly. On 2/20/19 11:44 AM, john Anderson wrote: > >    

Re: [Freesurfer] registration and resampling in native space

Yes,  if you run it with the --targ as orig.mgz for the given subject, then it will sample each run into the anatomical space (this can create enourmous data data files!). Alternatively, you can run preproc-sess with the --per-session flag and it will align all the runs to a single template but

Re: [Freesurfer] CAT12 surfaces on tkregister2 and Freeview

When you run mris_convert try adding --vol-geom orig.mgz where orig.mgz On 2/20/19 7:14 AM, Loucao, Ricardo wrote: > > External Email - Use Caution > > Dear FS experts and users, > > I’m having some troubles with CAT surfaces visualisation in > tkregister2 and Freeview. > > Context: I’ve

Re: [Freesurfer] Sections of Temporal Lobe not included

Is there a defect in those regions? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview On 2/20/19 9:33 AM, John Mc Fadden wrote: > > External Email - Use Caution > > Hi Douglas, > > Here are the rotated images > > -Original Message- > From: freesurfe

Re: [Freesurfer] Extracting anatomical locations for a set of RAS coordinates

For a volume, I would do it differently. In matlab [segcodes segnames ] = read_fscolorlut(); % read in the seg lookup table aparcaseg = MRIread('aparc+aseg.mgz'); % Load in the volume crs = round(inv(aparcaseg.tkrvox2ras)*[tkr tka tks 1]')+1; % convert your tkreg coords to col, row, and slice c

Re: [Freesurfer] mri_convert

External Email - Use Caution Hi Dr Greve, Thanks for the response. yes, I need to extract the acquisition times for kinetic modeling using PET surfer. Please I have two follow-up questions and I appreciate any highlights: - Are the acquisition times that PET surfer needs to be in

Re: [Freesurfer] mri_convert

On 2/21/19 12:56 PM, john Anderson wrote: > > External Email - Use Caution > > Hi Dr Greve, > > Thanks for the response. > yes, I need to extract the acquisition times for kinetic modeling > using PET surfer. Please I have two follow-up questions and I > appreciate any highlights: > -

[Freesurfer] recon-all -hires

Dear Freesurfer experts I was running recon-all command with hires flag for our high resolution fMRI data, but it has been in a constant status since yesterday. I copied the last few lines that are currently in my terminal. I had the same issue with another subject before, and I had to termina

Re: [Freesurfer] mris_preproc error: dimension mismatch

External Email - Use Caution It turns out I could run qcache on a unique surface file in the subject's folder. After a few tries with the surface file name it worked. Using tcsh command line I ran qcache on all of my subjects: cd your_study_group_data setenv SUBJECTS_DIR $PWD

Re: [Freesurfer] registration and resampling in native space

External Email - Use Caution Thanks a lot! Running preproc-sess with the --per-session flag is exactly was I was looking for! Now that my functional runs are correctly registered to a reference image (so, to each other) I need to register them to a dataset of ROIs that were created

Re: [Freesurfer] recon-all -hires

Hi MOna what was your full command line? And can you send us the recon-all.log file? cheers Bruce On Thu, 21 Feb 2019, Nasiriavanaki, Zahra wrote: Dear Freesurfer experts I was running recon-all command with hires flag for our high resolution fMRI  data, but it has been in a constant sta

[Freesurfer] dt_recon registration check

External Email - Use Caution Hello, I have run through dt_recon and want to use anatomically based segmentations (aseg) to create ROIs for the diffusion-weighted data using mri_vol2vol. I ran mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ $subj_dir/diffu

[Freesurfer] Data Analyst / Research Assistant Position at Child Mind Institute, New York {Disarmed}

External Email - Use Caution *The Autism Center of the Child Mind Institute **is inviting applications **for a Data Analyst position. The Data Analyst’s role is to assist and support the acquisition, manipulation, and analysis of data, as well as the reporting of brain imaging resu

[Freesurfer] Issue posting to Freesurfer support

External Email - Use Caution Hello, I am signed up to post emails to Freesurfer support list < freesurfer@nmr.mgh.harvard.edu> which I have cced in this email. However, when I submit my questions they do not seem to show up or go to the listserv. Is there someone I could contact t

[Freesurfer] QDEC Longitudinal Analysis: Missing spc option from dropdown menu

External Email - Use Caution Dear Freesurfer experts, I am having issues choosing the spc option for my QDEC two stage longitudinal analysis as it is not there. The spc files are all present in my participants files and the Qdecrc file is in the qdec subdirectory containing the

[Freesurfer] Alignment to ACPC

External Email - Use Caution Hello Freesurfer experts Freesurfer preprocessed data by(recon-all) are ACPC aligned? If not how can I align my files to ACPC? I read the documents but I am still very confused about the alignment and coordinate system in freesurfer. Thanks in advance

Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label

External Email - Use Caution Hello Bruce, I am just checking in as I am curious if there has been any update available regarding the entorhinal and perirhinal annot/labelling? I hope I haven't missed anything. Thank you! Yi Leng On Sun, Feb 10, 2019, 16:32 Yi Leng Fung wrote: