Re: [Freesurfer] freesurfer with infants MRI

Many thanks for your helpfulness, Dr. Fischl. Your information have been useful for me. Moreover, I will follow your suggestion: browsing on your website, I understand that Dr. Lilla Zollei could be the right person I can ask for more details. Best wishes Chiara Chiara Bulgar

[Freesurfer] more on comparing runs on the same scan

We have been able to establish that we are getting identical results when running recon-all -all on the same scan on different machine for the following: All .mgz files in directories mri, mri/orig, and mri/transforms, by comparing using mri_diff ... All of the .label and .annot files in director

Re: [Freesurfer] MNI coords in GLM cluster

There is not an easy way to do this. A couple of things you can do: First, convert the MNI152 coordinate to MNI305 coordinate. Then (1) load the cluster into tksurfer or freeview with fsaverage. fsaverage is in mni305 space, so you should be able to plug the coordinates into the RAS space. The

[Freesurfer] Freesurfer version 6.0

Dear Freesurfer experts, How may I get Freesurfer v 6 ? Thank you very much, Best wishes, Barbara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is

[Freesurfer] path.pd.trk format

Hello, I've noticed that in tracula 5.2 there's also a path.pd.trk file in the output directory. How can I read this file? I would like to read the actual splines and not the probabilistic distribution in path.pd.nii.gz. Thanks, Noam Peled ___ Freesurf

[Freesurfer] Correct_all_vols_4_sphinx_position

Hello, I'm a rookie and I had issues with the unpack_CIT script, so I went ahead and created the data structure similar to "bert testsubjects". I also converted my raw dicom files to mgz format. I'm currently trying to run "00.05_correct_all_vols_4_sphinx_position.csh" . Is there anything wron

Re: [Freesurfer] Extract LGI at MaxVertex of a significant Cluster, Effect sizes

On 02/03/2016 08:20 AM, Bittner, Nora wrote: > > Dear FreeSurfer Experts, > > I have two questions, which you can hopefully answer to: > > 1) > > I calculated several analyses with LGI as my dependent variable, > resulting in several significant clusters. > > Now, I would like to extract the ind

Re: [Freesurfer] unpacking error

Yes, dcmunpack does not take a -seqcfg argument, so specify each run separately And it can take a while. On 02/04/2016 01:42 PM, Ji Won Bang wrote: > Hi. > > When I tried dcmunpack: > dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ > $DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UN

Re: [Freesurfer] selxavg3-sess problem: SVD input matrix contains NaN

It appears that you do not have any events for condition 3. Is that correct? Check your par files. doug On 02/08/2016 08:28 PM, Mcnorgan, Christopher wrote: > Hi Doug, > Thanks for looking at this. The .mat file is attached. Can you send me the Xtmp.mat file? On 2/2/16 6:40 PM, Mcnor

Re: [Freesurfer] Reading values from overlays with PETcoreg

Hi Benjamin, do you still have a question about this? I lost the thread so please summarize the problem again. thanks doug On 02/09/2016 05:01 AM, Benjamin Spurny wrote: > Hello Doug, > > Thanks for your answer! > I already tried this workflow but basically I am interested in a > surface-based an

Re: [Freesurfer] fwhm issue with mri_glm-sim

When you run mri_glmfit, it computes an estimate of the FWHM from the residuals. In this case, the FWHM=46 eventhough you smoothed it by only 15. This can occur for a couple of reasons. One is that one or more subjects have bad data, another is that the data are inherently very smooth. Try run

Re: [Freesurfer] How to convert a surface label to .nii

Use mri_label2vol On 02/11/2016 09:17 AM, Afzal, Afsana wrote: > Hi, > > How can I convert a surface .label file to a .nii format? I'm using > mri_label2label in the following way but the output is always in > .label not .nii: > > mri_label2label > --srclabel dlpfc-lh.label > --outmask d

Re: [Freesurfer] comparison between two hemisphere in single

Please remember to include previous correspondence, otherwise I have no idea what this refers to thanks doug On 02/13/2016 06:10 AM, Ashkan Faghiri wrote: > Thank you Douglas for your reply. > > I have perforemed > > surfreg --s subj1 --t fsaverage_sym --lh > surfreg --s subj1--t fsaverage_sym --

Re: [Freesurfer] Freesurfer tool to automatically generate label surrounding a given vertex?

Another way to do this is to use mri_volsynth to create a surface overlay with a single vertex 1 and everything else 0, then use mri_surf2surf to smooth the overlay to create a disk on the surface, then use mri_binarize, then use mri_vol2label to create a surface label. for mri_volsynth, use --p

Re: [Freesurfer] path.pd.trk format

I've found an example how to read trk file with nibabel: > import nibabel as nib > > track_gen, hdr = nib.trackvis.read(trk_file, as_generator=True) > > tracks = [] > while True: > try: > track = next(track_ge

Re: [Freesurfer] Fwd: Specifying color table file

If you run it with --help, you will find the info you need On 02/15/2016 02:02 PM, Faeze Vedaei wrote: > Hi Freesurfer experts, > > In order to using mris_label2annot command to create annot files, I've > got an error: need to specify color table file. Does anyone know how > can I create and spe

Re: [Freesurfer] Freesurfer version 6.0

We don't have a v6 ready. You can get a development version, you just have to keep in mind that it is a snapshot and that the software will change without notice. On 02/16/2016 02:12 PM, Barbara Kreilkamp wrote: > Dear Freesurfer experts, > > How may I get Freesurfer v 6 ? > > Thank you very muc

Re: [Freesurfer] mri_annotation2label

On 02/15/2016 12:20 PM, Worker, Amanda wrote: > > Hi All, > > > I am trying to run a vertex-wise analysis on a pre-defined ROI - the > caudal anterior cingulate label as defined by the Desikan atlas. I > have used mri_annotation2label to get these labels for each subjects > ./label directory.

Re: [Freesurfer] tkregister visualization issue

Can you run other tk commands like tkmedit and tksurfer? On 02/09/2016 12:23 PM, Philip Brandner wrote: > > Dear Freesurfer team, > > > I encountered a visualization error with tkregister-sess after trying > to look at the > > overlays of my 1st level analysis in a standard fMRI block designed >

[Freesurfer] Reference about: MeanCurv, GausCurv, FoldInd, CurvInd?

H! I am working with data which is an output from the FreeSurfer processing. I would like to kindly ask you to refer me to materials / precise "mathematical" definitions that could help to understand what are the following parameters: * ?MeanCurv - Integrated Rectified Mean Curvature, *

[Freesurfer] v.6.0 Permissions Error

Hello all, I am in the middle of a FreeSurfer v.6.0 longitudinal analysis, running on the Martinos cluster, and I received an error today during the (-base) template creation step regarding a file that the pipeline calls upon: GCAread(/usr/local/freesurfer/stable6/average/RB_all_

Re: [Freesurfer] v.6.0 Permissions Error

ok, try now On 02/16/2016 04:38 PM, Grafe,Brendan P. (BIDMC - Neurology) wrote: > > Hello all, > > I am in the middle of a FreeSurfer v.6.0 longitudinal analysis, > running on the Martinos cluster, and I received an error today during > the(–base) template creation step regarding