Re: [Freesurfer] Surface-based analysis of tfMRI

External Email - Use Caution Got it. Thank you very much for your patient reply. Best wishes On Tue, 23 Oct 2018 at 18:59, Bruce Fischl wrote: > can you clarify what you mean? We produce two cortical parcellations by > default (one from Christophe Destrieux and one from Rahul

Re: [Freesurfer] Surface-based analysis of tfMRI

can you clarify what you mean? We produce two cortical parcellations by default (one from Christophe Destrieux and one from Rahul Desikan). What kind of parcellation would you want? Note that the parcellation is not done by propagating a template to the individual. Rather we extract an array of

Re: [Freesurfer] Surface-based analysis of tfMRI

External Email - Use Caution I see. Thank you very much. Another question is if I can use other template for parcellation when I use recon-all? On Tue, 23 Oct 2018 at 13:42, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > You specify the input you want selxavg3-sess

Re: [Freesurfer] How to export the image and label

Hi Jackie 1. We don't currently support dicom as an output format, sorry. 2. You can manually edit the boundaries using freeview. 3. I guess you could use mri_tessellate or mri_mc to builda surface of any of the brainstem structures if you want cheers Bruce On Tue, 23 Oct 2018, Min Zhang

[Freesurfer] How to export the image and label

External Email - Use Caution > Dear FreeSurfer Team : > I used the freeSurfer brainstem structure to segment the brainstem from > the MRI successfully. But I have several questions as followed: > > 1. I want to export this data in dcm file with all the ROI information, > what

Re: [Freesurfer] Physiological Noise Regression from rsMRI

you can give it multiple -nuisreg options, so keep them in separeate files if you want On 10/23/18 12:23 PM, Meisler, Steven Lee wrote: Also, I currently have one regressor file for cardiac noise and one for respiratory, each with multiple columns (each column representing a Fourier

Re: [Freesurfer] Physiological Noise Regression from rsMRI

Skull stripping? Are you talking about functional or anatomical data? This only applies to FSFAST, not recon-all. You'd run the fsfast preprocessing as normal. On 10/23/18 12:21 PM, Meisler, Steven Lee wrote: Thank you! At what point in the processing pipeline should this happen? For example,

Re: [Freesurfer] Surface-based analysis of tfMRI

You specify the input you want selxavg3-sess to use. Otherwise, it will try to look for things that have been preprocessed. On 10/23/18 12:17 PM, Zhi Li wrote: External Email - Use Caution Thank you. May I ask what do we use the flag -funcstem for? I found that there are similar flags

Re: [Freesurfer] Physiological Noise Regression from rsMRI

Also, I currently have one regressor file for cardiac noise and one for respiratory, each with multiple columns (each column representing a Fourier decomposition term). Should I consolidate these two txt files into one txt file, or should I call -nuisreg twice? Thanks again. Best, Steven

Re: [Freesurfer] Physiological Noise Regression from rsMRI

Thank you! At what point in the processing pipeline should this happen? For example, should this happen before or after skull-stripping? Best, Steven From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: Tuesday, October

Re: [Freesurfer] Surface-based analysis of tfMRI

External Email - Use Caution Thank you. May I ask what do we use the flag -funcstem for? I found that there are similar flags in preproc-sess, -mcin, -stcin, etc. Sorry I am a beginner of FreeSufer and not clear about some terms such as 'stem' in both preproc-sess and

Re: [Freesurfer] Running DICOMS versus FreeSurfer5.3 Output

If you have edits you want to save, then you can re-run over 5.3. It should work regardless, but it will be a little cleaner if you start from scratch. On 10/18/18 4:34 AM, Scheffler, F, Mev [fre...@sun.ac.za] wrote: External Email - Use Caution Dear FreeSurfer

Re: [Freesurfer] Physiological Noise Regression from rsMRI

You will just need to create a text file with one or more columns, one for each regressor put this in the run folder (same folder where the raw data are). When you run mkanalysis-sess, add -nuisreg filename N where N is the number of columns you want to include On 10/18/18 10:34 AM, Meisler,

Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

They are the same thing underneath. On 10/18/18 11:12 AM, Azeez, Azeezat wrote: External Email - Use Caution Thank you for the response. Which smoothing option would you recommend, there is one in mris_preproc, but there is also mris_smooth. Thanks You On Wed, Oct 17, 2018 at 1:56 PM

Re: [Freesurfer] Mapping a custom measure to the pial surface of fsaverage

You can use preproc-sess and specify the --meas flag. Run with --help for more info. On 10/18/18 2:08 PM, ts...@rcmd.org wrote: > External Email - Use Caution > > Dear FreeSurfer experts, > > I have created a custom measure on the pial surface of a number of subjects, > and I would

Re: [Freesurfer] errors running mri_glmfit

You have no subjects in the DIATD-DEVC-sexM class On 10/18/18 1:53 PM, Azeez, Azeezat wrote: External Email - Use Caution Hello I keep getting the same error and am not sure how to address the issue. I have attached the design matrix and the FSGD file and contrast file of interest

Re: [Freesurfer] FreeSurfer error at selxavg3-sess

Not sure what the problem is. The "unrecognized" warning is not a problem. What is your mkanalysis-sess command line? What version of FS are you running? You can try just deleting the LH and re-running mkanalysis and selxavg On 10/20/18 12:33 PM, elahe' yargholi wrote: External Email -

Re: [Freesurfer] Surface-based analysis of tfMRI

Yes. When you run mkanalysis-sess, you may still have to use the -funcstem On 10/23/18 10:06 AM, Zhi Li wrote: External Email - Use Caution I see. Can I add the flag -nomc to skip motion correction? If I have done the slice timing, realignment and denoising, can I use the following

Re: [Freesurfer] Surface-based analysis of tfMRI

External Email - Use Caution I see. Can I add the flag -nomc to skip motion correction? If I have done the slice timing, realignment and denoising, can I use the following command to do registration, normalization and smoothing? *preproc-sess -s sess01 -fsd bold -nomc -nostc

Re: [Freesurfer] Myelinated cortical thickness ratio map

External Email - Use Caution Hi Matt, Many thanks for your prompt reply, you are right. Any tips on how I could do that? Should I regress out cortical thickness from my myelin maps at the individual level, save the individual output myelin maps and run analyses on the latter?