[Freesurfer] FSFAST Download

External Email - Use Caution Hello, I’m attempting to download FSFAST on my non-MGH computer using the instructions here

Re: [Freesurfer] fsfast percent signal change

External Email - Use Caution Use the cespct.nii.mgz file On 5/24/2023 10:18 AM, Maria Czarnecka wrote: External Email - Use Caution Dear experts, I struggle with the functional analysis in Freesurfer. How can I calculate the percent signal change in a specific

[Freesurfer] fsfast percent signal change

External Email - Use Caution Dear experts, I struggle with the functional analysis in Freesurfer. How can I calculate the percent signal change in a specific contrast in an ROI? I will be grateful for your suggestions (especially if you point toward a specific function). Kind

Re: [Freesurfer] FSFAST: wrong brain mask in preproc

External Email - Use Caution Thank you for clarifying. Elmira On Wed, Apr 26, 2023 at 6:44 PM Douglas N. Greve wrote: > External Email - Use Caution > > Yes, this is the expected behavior, ie, it should cover only subcortical > GM regions. It is expected that cortical

Re: [Freesurfer] FSFAST: multiple resting state runs

External Email - Use Caution if you set up the data in the fsfast format, eg, subject/rest/001 subject/rest/002 etc, then it will handle it automatically On 4/26/2023 12:30 PM, Elmira Hassanzadeh wrote: External Email - Use Caution Hi, How do we analyze multiple 

Re: [Freesurfer] FSFAST: multiple resting state runs

External Email - Use Caution it will also handle the concatenation On 4/26/2023 12:30 PM, Elmira Hassanzadeh wrote: External Email - Use Caution Hi, How do we analyze multiple resting state runs for a subject at once? - do we need certain folder structure/naming? -

Re: [Freesurfer] FSFAST: wrong brain mask in preproc

External Email - Use Caution Yes, this is the expected behavior, ie, it should cover only subcortical GM regions. It is expected that cortical regions will be handled with the surface based analysis. You can recombine the results at the end with vlrmerge. On 4/26/2023 12:22

[Freesurfer] FSFAST: multiple resting state runs

External Email - Use Caution Hi, How do we analyze multiple resting state runs for a subject at once? - do we need certain folder structure/naming? - do we do concatenation? Thanks, Elmira ___ Freesurfer mailing list

[Freesurfer] FsFast retinotopy and its flags

External Email - Use Caution Dear Freesurfer experts, I am attempting to run an old-fashioned polar angle retinotopy analysis through FsFast. Unsurprisingly, the tutorials I've found on the topic are somewhat outdated (>10 years ago) and seem to suggest employing flags that

Re: [Freesurfer] FSFAST first level covariates

...@mgh.harvard.edu> Reply-To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, August 30, 2022 at 7:38 AM To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re:

Re: [Freesurfer] FSFAST first level covariates

22 at 7:38 AM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] FSFAST first level covariates Oh, I think I see now. In realty, each trial is either self or not self and then you have a separate valence measure, so your coding should be 1. Self-offset 2. SelfValenc

Re: [Freesurfer] FSFAST first level covariates

) would be different from condition 5 (valence ratings only)? Incredibly helpful, Doug- thank you so much! From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Tuesday, August 30, 2022 at 7:38 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re:

Re: [Freesurfer] FSFAST first level covariates

; *Reply-To: *Freesurfer support list *Date: *Sunday, August 28, 2022 at 1:07 PM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] FSFAST first level covariates I was under the impression that Self and Valence were ratings from the same event (in that mail archive, they were dif

Re: [Freesurfer] FSFAST first level covariates

(not self-relevant)? Could we code it as 2 (self-relevant) and 1 (not self-relevant)? Many thanks!! From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Sunday, August 28, 2022 at 1:07 PM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer

Re: [Freesurfer] FSFAST first level covariates

;freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] FSFAST first level covariates Those look like they are the same coding scheme. What is different? You can only have one offset. The Self vs Valence -a 2 -a 4 is not testing for an interaction. If you want an interaction you

Re: [Freesurfer] FSFAST first level covariates

u" Subject: Re: [Freesurfer] FSFAST first level covariates Those look like they are the same coding scheme. What is different? You can only have one offset. The Self vs Valence -a 2 -a 4 is not testing for an interaction. If you want an interaction you have to create a new variable which is Self

Re: [Freesurfer] FSFAST first level covariates

I describe below), that would also be helpful to know. Thanks! Angela *From: * on behalf of Angela Fang *Reply-To: *Freesurfer support list *Date: *Monday, August 1, 2022 at 4:35 PM *To: *Freesurfer support list *Subject: *Re: [Freesurfer] FSFAST first level covariates *Exte

Re: [Freesurfer] FSFAST first level covariates

To: Freesurfer support list Subject: Re: [Freesurfer] FSFAST first level covariates External Email - Use Caution Hi Doug, Nevermind to my first question! I read this post (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web

Re: [Freesurfer] FSFAST first level covariates

Subject: Re: [Freesurfer] FSFAST first level covariates Thanks Doug. This wiki page is extremely helpful. However, my question is about individual subject responses. I could see how you could include a summary (e.g., average) value of the parametric variable across subjects in your “weight” column

Re: [Freesurfer] FSFAST first level covariates

y, July 28, 2022 at 10:25 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] FSFAST first level covariates Yes, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation On 7/25/2022 6:56 PM, Angela Fang wrote: External Email - Use Caution Hi Fre

Re: [Freesurfer] FSFAST first level covariates

Yes, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation On 7/25/2022 6:56 PM, Angela Fang wrote: External Email - Use Caution Hi Freesurfer community, I have run participants through an event-related fMRI task in which subjects rate whether trait adjectives

[Freesurfer] FSFAST first level covariates

External Email - Use Caution Hi Freesurfer community, I have run participants through an event-related fMRI task in which subjects rate whether trait adjectives are descriptive of themselves or not, and afterwards asked them to rate each trait word on emotional valence. Is it

Re: [Freesurfer] FSFAST (mkcontrast-sess) with Octave

Hi Lauri, I was able to run this successfully here on 7.2. What version of FS are you using? Can you send /tmp/mkcontrast2.28236.m (if still there)? doug On 8/17/2021 3:10 PM, Lauri Tuominen wrote: > External Email - Use Caution > > Dear Surfers, > I am trying to run fsfast

[Freesurfer] FSFAST (mkcontrast-sess) with Octave

External Email - Use Caution Dear Surfers, I am trying to run fsfast mkcontrast-sess with octave. I used the following command: "mkcontrast-sess -analysis ../mkanalysis/ftap.sm05.lh -contrast ftap -a 1 -octave" I get the output below. I wonder if you could help me out? Am I

Re: [Freesurfer] FsFast Question

Not directly as an external regressor. You would have to extract the info and create a waveform, one value for each TR in the external regressor file. You might also want to convolve it with a hemodynamic response function On 1/8/20 11:15 AM, Swetara Joshi wrote: > > External Email -

[Freesurfer] FsFast Question

External Email - Use Caution Hello, I am new to fmri processing/FsFast and I had a question on creating nuisance variables. Is it possible to set a block-design task fMRI paradigm file as a nuisance variable, so that it can be inputted at a .dat file for the mkanalysis-sess

Re: [Freesurfer] FSFAST registration

On 12/30/2019 7:55 PM, Star Xi wrote: External Email - Use Caution Dear FS experts, I’m processing the task-related fMRI using FS-FAST. I check the quality assurance and modified some subjects’ registration file(named new one as “register_manual.lta”). Then I do the first level

[Freesurfer] FSFAST registration

External Email - Use Caution Dear FS experts, I’m processing the task-related fMRI using FS-FAST. I check the quality assurance and modified some subjects’ registration file(named new one as “register_manual.lta”). Then I do the first level analysis and

Re: [Freesurfer] fsfast no run directories

setenv SUBJECTS_DIR /usr/local/freesurfer/subjects Linux andraderenew 5.0.0-36-generic #39~18.04.1-Ubuntu SMP Tue Nov 12 11:09:50 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux /home/andraderenew/Downloads/barrios/project /usr/local/freesurfer/fsfast/bin/preproc-sess -s sess1 -fsd bold -stc up -surface

[Freesurfer] fsfast no run directories

x86_64 GNU/Linux /home/andraderenew/Downloads/barrios/project /usr/local/freesurfer/fsfast/bin/preproc-sess -s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run vie nov 29 07:33:28 CET 2019 instem   f mc   1 f fmcpr stc  1    fmcpr fmcpr.up sm   0    mask 1   brain sess

Re: [Freesurfer] FSFAST group analysis problem: dimension mismatch between y and X

Can you check the modification time of ~/audio/all/audio.lh/tones/ces.nii.gz ? Try deleting it and rerunning isxconcat-sess. The only other thing that I can think of is that some of the individual ces files have multiple frames. You can check that with mri_info --nframes

[Freesurfer] FSFAST group analysis problem: dimension mismatch between y and X

External Email - Use Caution Hi Freesurfer experts I'm having a problem running an FSFAST group analysis. When I try to run the second level GLM, I get the following error: keri@buddha:~/audio_108_no_stc_tau1,5$ mri_glmfit --y ~/audio/all/audio.lh/tones/ces.nii.gz --wls

Re: [Freesurfer] FSFAST poor registration

External Email - Use Caution Good thing it's not the software :) Also makes it easier for me to fix. In my script there was one tiny mistake - the anatomical image for one subject was repeated each time instead of using the files for different subjects. I ran recon-all 100+ times

Re: [Freesurfer] FSFAST poor registration

Yes, that file is the only thing linking the functional to the anatomical. It's too bad you messed up the files, but I'm relieved it was not my software:). On 1/25/19 5:09 AM, Keri Woods wrote: External Email - Use Caution Hi Douglas Thanks very much for getting back to me. I created

Re: [Freesurfer] FSFAST poor registration

External Email - Use Caution Hi Douglas Thanks very much for getting back to me. I created new separate directories and re-processed one of the problem subjects individually, and the registration worked well. So the problem is that the anatomical and functional images come from

Re: [Freesurfer] FSFAST poor registration

Can you tar up the anatomical and functional analyses and send them to me through our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2/ when it asks for an email of the recipient, use gr...@nmr.mgh.harvard.edu On 1/23/19 5:57 AM, Keri Woods wrote: > > External Email - Use Caution

Re: [Freesurfer] FSFAST poor registration

External Email - Use Caution I meant some are nearly perfect. On Wed, Jan 23, 2019 at 11:49 AM Keri Woods wrote: > Hi Douglas > > Thanks for the response. > > No, some of the registrations are fine. Some are close, but not perfect, > while others are very bad. > > I've checked

Re: [Freesurfer] FSFAST poor registration

External Email - Use Caution Hi Douglas Thanks for the response. No, some of the registrations are fine. Some are close, but not perfect, while others are very bad. I've checked the subjectname file for some subjects with poor registration (eg 20_101), and they are correct.

Re: [Freesurfer] FSFAST poor registration

Are you saying that all of them have bad registrations? Some of them (eg, 20_1, 20_10) look like they should be good. Others (eg, 20_101) look like they could be bad. For the bad ones, are you totally sure that the subjetname file has the correct name of the subject? On 1/21/19 3:19 AM, Keri

Re: [Freesurfer] FSFAST poor registration

What version of FS are you using? version 6 initializes with mri_coreg (the FS equivalent of spm_coreg). On whole-brain data, I've found this to be very robust. Is your data whole-brain? On 1/18/19 5:10 AM, Keri Woods wrote: External Email - Use Caution Hi I have a problem very

[Freesurfer] FSFAST poor registration

External Email - Use Caution Hi I have a problem very similar to this one: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23206.html I've tried the suggestions given there, but it didn't fix my problem. I'm running the FSFAST preproc-sess stream and the quality

Re: [Freesurfer] fsfast preproc-sess: viewing preproc surface outputs

You can load them in freeview through tksurferfv, something like tksurferfv fsaverage lh inflated -aparc -ov fmcpr.odd.sm5.fsaverage.lh.nii.gz There's not much to see:) On 10/16/2018 03:00 PM, Jacob Matthews wrote: > > External Email - Use Caution > > Hi FS Team, > > We are running our

[Freesurfer] fsfast preproc-sess: viewing preproc surface outputs

External Email - Use Caution Hi FS Team, We are running our first fsfast pipeline, and starting with a single subject to test everything. We successfully ran preproc-sess with the following command: preproc-sess -s 11987_20180731 -surface fsaverage lhrh -mni305 -fwhm 5 -per-run

Re: [Freesurfer] FSFAST, Beta values and Percent Signal Change questions

On 4/16/18 11:56 AM, Sarah Cole wrote: Hi Doug, I need your recommendations on two topics. I really appreciate your help. 1.) I have two runs of the same experiment, each for about 12 minutes. These 2 runs are different only in the presentation order of the stimuli. I also have one

[Freesurfer] FSFAST, Beta values and Percent Signal Change questions

Hi Doug, I need your recommendations on two topics. I really appreciate your help. 1.) I have two runs of the same experiment, each for about 12 minutes. These 2 runs are different only in the presentation order of the stimuli. I also have one localizer session which first, I calculated my

Re: [Freesurfer] [FSFAST]

Thank you, i will! Walid > On Apr 10, 2018, at 8:03 AM, Douglas N. Greve wrote: > > You can do it with the tpexclude file. Do a search through the archives > for docs on how to use it > > > On 04/09/2018 06:56 PM, Walid Yassin wrote: >> Hello Doug, >> >> Thank you

Re: [Freesurfer] [FSFAST]

You can do it with the tpexclude file. Do a search through the archives for docs on how to use it On 04/09/2018 06:56 PM, Walid Yassin wrote: > Hello Doug, > > Thank you for your previous answer. > I have another question in the mkanalysis. When I run mkanalysis is it > possible to analyse

Re: [Freesurfer] [FSFAST]

Hello Doug, Thank you for your previous answer. I have another question in the mkanalysis. When I run mkanalysis is it possible to analyse only a part of my run? I mean if my stimuli was 100s per run, can i tell mkanalysis to ignore the first 20s and the last 30s and analyse the 50 in the

Re: [Freesurfer] [Freesurfer/FSFAST]

<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgr...@mgh.harvard.edu> Sent: Wednesday, April 4, 2018 3:49 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Freesurfer/FSFAST] but using what program? mri_convert? Can you try converting it again and

Re: [Freesurfer] [Freesurfer/FSFAST]

. *From:* freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgr...@mgh.harvard.edu> *Sent:* Wednesday, April 4, 2018 3:34 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] [Freesurfer/FSFAST]

Re: [Freesurfer] [Freesurfer/FSFAST]

pril 4, 2018 3:34 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Freesurfer/FSFAST] The version should not matter here. How did you create /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii ? On 4/3/18 7:51 PM, Dave Yas wrote: Sorry i forgot to mention tha

Re: [Freesurfer] [Freesurfer/FSFAST]

[Freesurfer] [Freesurfer/FSFAST] Is the disk full? On 4/3/18 6:48 PM, Dave Yas wrote: Yes, the file exists! Here is the full output: -- preproc-sess logfile is log/preproc-sess.sess01.log --

Re: [Freesurfer] [Freesurfer/FSFAST]

day, April 3, 2018 11:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Freesurfer/FSFAST] Is the disk full? On 4/3/18 6:48 PM, Dave Yas wrote: Yes, the file exists! Here is the full output: -- preproc-sess lo

Re: [Freesurfer] [Freesurfer/FSFAST]

.harvard.edu Subject: Re: [Freesurfer] [Freesurfer/FSFAST] Is the disk full? On 4/3/18 6:48 PM, Dave Yas wrote: Yes, the file exists! Here is the full output: -- preproc-sess logfile is log/preproc-ses

Re: [Freesurfer] [Freesurfer/FSFAST]

/Users/Studies/Directory/Study_Directory /Applications/freesurfer/fsfast/bin/preproc-sess -fsd bold -per-run -s sess01 -fwhm 5 Tue Apr  3 10:11:25 JST 2018 instem   f mc   1     f fmcpr stc  0     fmcpr sm   1 fmcpr fmcpr.sm5 mask 1   brain sess01 Template - mktemplate-sess

Re: [Freesurfer] [Freesurfer/FSFAST]

/freesurfer/fsfast/bin/preproc-sess -fsd bold -per-run -s sess01 -fwhm 5 Tue Apr 3 10:11:25 JST 2018 instem f mc 1 f fmcpr stc 0 fmcpr sm 1 fmcpr fmcpr.sm5 mask 1 brain sess01 Template - mktemplate-sess -s sess01 -d /Users/Studies/Directory/Study_Directory -fsd

Re: [Freesurfer] [Freesurfer/FSFAST]

does that file exist? CAn you send the full terminal output? On 4/2/18 9:53 PM, Dave Yas wrote: Hi, I am running preproc-sess on one subject. I got the following error after running preproc-sess: Error: niiRead(): error reading from

[Freesurfer] [Freesurfer/FSFAST]

Hi, I am running preproc-sess on one subject. I got the following error after running preproc-sess: Error: niiRead(): error reading from /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii My PWD: /Users/Studies/Directory/Study_Directory My echo $SUBJECTS_DIR:

Re: [Freesurfer] [FSFAST]

Sorry, yes you can use an A-B blocked paradigm. Run mkanalysis-sess -help to get more info On 3/20/18 4:28 AM, Walid Yassin wrote: Hello all, I would like to pose my question again in case it got missed. Thank you. WY On Mon, Mar 19, 2018 at 3:47 PM, Walid Yassin

Re: [Freesurfer] [FSFAST]

Hello all, I would like to pose my question again in case it got missed. Thank you. WY On Mon, Mar 19, 2018 at 3:47 PM, Walid Yassin wrote: > Hi Doug, > > Is it possible to run retinotopy-like analysis to reveal areas in the > brain responsible for a certain phase of

[Freesurfer] [FSFAST]

Hi Doug, Is it possible to run retinotopy-like analysis to reveal areas in the brain responsible for a certain phase of a presented stimuli? Say, instead of presenting 0 - 360 degrees of rotating wedge per cycle, we would like to present arbitrary scale of 0 - 100 of a particular stimulus

Re: [Freesurfer] FSFAST

Only fmc.odd.sm5.nii.gz is in the same dimensions as the f.nii.gz. However, I found a flag in the selxavg3 (-no-con-ok)that I do not need to specify a contrast. If I am not mistaken, all is good now. Thank you for your response. On Sat, Feb 3, 2018 at 2:03 PM, Douglas Greve

Re: [Freesurfer] FSFAST

That file should be in the same dimensions, no? On 1/30/18 12:19 AM, Ashley Cole wrote: I just noticed that that file "fmc.odd.sm5.nii.gz" is created after selxavg3-sess. I was wondering how can I preprocess the functional image and have the output with the same dimension as the f.nii.gz

Re: [Freesurfer] FSFAST

I just noticed that that file "fmc.odd.sm5.nii.gz" is created after selxavg3-sess. I was wondering how can I preprocess the functional image and have the output with the same dimension as the f.nii.gz without performing any contrasts. I just need to look at the signal in some ROIs without

[Freesurfer] FSFAST

Hello, I have several nifti files. I have preprocessed some of them before. I used this command: preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 -fwhm 5 -per-session -force The output files contained fmc.odd.sm5.self.lh.nii.gz, fmc.odd.sm5.self.rh.nii.gz,

Re: [Freesurfer] fsfast

Those are two different things. The --seg is the name of the segmetation (eg, aparc+aseg.mgz). --segid is the index in that segmentation to use On 8/2/17 5:23 PM, John Anderson wrote: Thank you Doug, One last question please in the command fcseed-config -segid 1010 -fcname

Re: [Freesurfer] fsfast

Thank you Doug, One last question please in the command fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg mean.L_Posteriorcingulate.config Instead of using segid. it is suggested in the help of fcseed that I can use the flag "seg segmentation" which is aparac+aseg

Re: [Freesurfer] fsfast

I still don't understand what you mean. in any event, fsfast is set up only to do seed-based FC. On 8/2/17 5:14 PM, John Anderson wrote: I mean instead of using seed like cingulate gyrus. Can I use the whole brain (e.g. wmparc.mgz)? what do you mean by functional connectivity if it is not

Re: [Freesurfer] fsfast

I mean instead of using seed like cingulate gyrus. Can I use the whole brain (e.g. wmparc.mgz)? what do you mean by functional connectivity if it is not seed based. > Original Message > Subject: Re: fsfast > Local Time: August 2, 2017 5:01 PM > UTC Time: August 2, 2017 9:01 PM

Re: [Freesurfer] fsfast

what do you mean by functional connectivity if it is not seed based? On 8/2/17 5:01 PM, John Anderson wrote: Hi Doug, thank you for your response. The steps in link that you provided is for a seed based functional connectivity analysis. I aim to compare the functional connectivity between

Re: [Freesurfer] fsfast

Hi Doug, thank you for your response. The steps in link that you provided is for a seed based functional connectivity analysis. I aim to compare the functional connectivity between two groups without using seeds similar to what we do in surface based analysis between two groups to compare

Re: [Freesurfer] fsfast

Are you following these steps? http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough When you make your analysis, you need to include something like -taskreg L_Posteriorcingulate.dat Then when you run isxconcat-sess, you include this as the contrast. See the wiki

Re: [Freesurfer] FSFAST (plot-twf-sess)

There are no easy ways to create a cut off. This is still a major question in fMRI analysis, esp for resting state. On 7/31/17 2:58 PM, John Anderson wrote: Dear Dr Greeve, I am new to FSFAST so I highly appreciate your response. I have resting state fMRI data and I am following the steps as

[Freesurfer] fsfast

Dear Dr Greve, I am new to FSFAST so I highly appreciate your response. I have resting state fMRI data and I am following the steps as reported in wiki. I want to study the difference in functional connectivity between two groups My questions are regarding motion evaluation and the contrasts. 1.

[Freesurfer] FSFAST (plot-twf-sess)

Dear Dr Greeve, I am new to FSFAST so I highly appreciate your response. I have resting state fMRI data and I am following the steps as reported in wiki. My questions is regarding motion evaluation. The attached figure is an output of "plot-twf-sess". 1. Given the plotted data can we say that

Re: [Freesurfer] FSFAST Full Model Residuals?

Actually, just noticed that this is an option in selxavg3-sess, never mind! On Wed, Jun 7, 2017 at 9:07 PM, Taylor, Johnmark < johnmarktay...@g.harvard.edu> wrote: > Hello, > > I had a quick question. Is there a way to make FSFAST output a 4D volume > of all the residuals? In other words: is

Re: [Freesurfer] FSFAST

On 5/5/17 5:06 AM, John Anderson wrote: Dear Doug, I have Bold fMRI data (6 minutes of acquisition which is equal to 180 volume for every run). The total number for images is 140 (50 controls and 90 patients). I plan to use FSFAST (FS V6.0) to study: 1. The difference between the groups in

[Freesurfer] FSFAST

Dear Doug, I have Bold fMRI data (6 minutes of acquisition which is equal to 180 volume for every run). The total number for images is 140 (50 controls and 90 patients). I plan to use FSFAST (FS V6.0) to study: 1. The difference between the groups in global functional connectivity 2. Seed-based

Re: [Freesurfer] [FSFAST] Matlab parallel

That should work (the env var is FSF_OUTPUT_FORMAT). You will also need to set it in your linux shell before running any of the scripts On 02/03/2017 09:51 AM, Seung-Goo KIM wrote: > Hi all, > > So this is a question about running FAST through matlab parallel > desktop: I know it is very funny

Re: [Freesurfer] [FSFAST] Matlab parallel

+Self-update: I figured out “.nii” works well. I thought “.mgz" should work well, but "preproc-sess” tried to read “template.mgz.nii” while it creates “template.nii”. So just the simple format “.nii” works well even in a harsh virtual environment (e.g.,matlab>parallel-workers>bash>csh>matlab).

[Freesurfer] [FSFAST] Matlab parallel

Hi all, So this is a question about running FAST through matlab parallel desktop: I know it is very funny (and inefficient) because I open up a bash in the matlab to run a csh script that generates and runs a matlab code, but just I’m familiar with matlab in doing many things including string

Re: [Freesurfer] [FSFAST] Contrast percent map

you have the right idea, but it is cespct = 100*contrast/baseline The baseline is the mean offset of the fMRI, the contrast is the deviation from baseline On 2/1/17 4:49 AM, Seung-Goo KIM wrote: Dear all, I wish to know how “cespct.nii.gz” is computed in selxavg3-sess. I thought it

[Freesurfer] [FSFAST] Contrast percent map

Dear all, I wish to know how “cespct.nii.gz” is computed in selxavg3-sess. I thought it computes something like a relative change like: cespct = (contrast-baseline)/baseline*100, but I cannot figure out what was taken for the baseline. I thought it could be mean beta for constant terms

Re: [Freesurfer] FSFAST ROI atlas

<freesurfer@nmr.mgh.harvard.edu> Date: Thursday, August 18, 2016 at 8:55 AM To: "Harms, Michael" <mha...@wustl.edu> Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FSFAST ROI atlas Hi Michael- Thanks very much for the file. Is

Re: [Freesurfer] FSFAST ROI atlas

rfer@nmr.mgh.harvard.edu>, "Harms, > Michael" <mha...@wustl.edu> > > Subject: Re: [Freesurfer] FSFAST ROI atlas > > Hi Michael- Is there anyway I can get those Gordon parcellation annot > files? > > Cheers, > Sabin Khadka > > On Wed, Aug 17, 2016 at 10:59 AM

Re: [Freesurfer] FSFAST ROI atlas

eesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu > > > Date: Wednesday, August 17, 2016 at 9:55 AM > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] FSFAST ROI atlas > > I don't

Re: [Freesurfer] FSFAST ROI atlas

behalf of Doug Greve <gr...@nmr.mgh.harvard.edu> Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, August 17, 2016 at 9:55 AM To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurf

Re: [Freesurfer] FSFAST ROI atlas

I don't know anything about the Power atlas. For the HCP, if they have it in annotation format, then you can run mri_aparc2aseg to map it into the anatomical volume, then specify that volume when you run fcseed-config. To get the mri_aparc2aseg command line, look in the recon-all to find out

Re: [Freesurfer] FSFAST ROI atlas

Hi Doug- Do you think it is possible to use these atlas? If so could you point me to steps that needed to be done. Thanks for your help! Cheers, Sabin Khadka On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve wrote: > I have not used them myself. > > On 8/15/16 10:23

Re: [Freesurfer] FSFAST ROI atlas

I have not used them myself. On 8/15/16 10:23 AM, Sabin Khadka wrote: HI all- I am using FSFAST to extract ROI time series values for further connectivity analysis. I've used Desikan, Destriuex and DKT atlas. However, I was wondering if anyone has used Power et.al 2011 rois

[Freesurfer] FSFAST ROI atlas

HI all- I am using FSFAST to extract ROI time series values for further connectivity analysis. I've used Desikan, Destriuex and DKT atlas. However, I was wondering if anyone has used Power et.al 2011 rois and/or HCP's newly defined 180/per hemi rois to extract time series data. If so could you

Re: [Freesurfer] FSFAST error: ERROR: fast_selxavg3() failed\n

atlab” in the command window, nothing happens. My $PATH structure is a s follows: echo $PATH /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local

Re: [Freesurfer] FSFAST error: ERROR: fast_selxavg3() failed\n

Is matlab in your path? What happens if you type which matlab at the command line? On 07/08/2016 12:34 AM, ERIK JAHNER wrote: > > Hello FreeSurfer Developers, > > > This is Erik Jahner, I’m attempting to complete the final step in the > tutorial concerning FSFast Functional connectivity

[Freesurfer] FSFAST error: ERROR: fast_selxavg3() failed\n

 fc.lpccseed.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5  -mcextreg -polyfit 5 -nskip 4 -fsd rest -TR 2 -per-runSTEP 8selxavg3-sess -s subj439rest -a fc.lpccseed.surf.lhselxavg3-sess log file /Applications/freesurfer/fsfast

Re: [Freesurfer] FSFAST- Cerebellum

What is the problem with the orientation? The little letters indicate that the orientation is correct. fslview ignores the orientation when displaying so it might come out upside down. On 07/05/2016 01:35 PM, Sabin Khadka wrote: > > Hi Doug, As you suggested I mapped fmri into the anatomical

Re: [Freesurfer] FSFAST time series extraction

Hi Doug, Yes. Dr. Yeo Thomas helped me figuring out ways to extract ROI values from Buckner 2011 7 Cerebellar network. Please see below for the steps I performed to extract time series from Buckner 2011 7 Cerebellar networks. If you could give your thoughts on the steps/process that'd be great.

Re: [Freesurfer] FSFAST time series extraction

has this question been answered? On 06/17/2016 09:42 AM, curry_sa...@yahoo.com wrote: > Hi all, > > I am trying to extract mean time series BOLD data using FSFAST from > Cortical ROIs + sub cortical ROIs and cerebellum. > > preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 >

Re: [Freesurfer] FSFAST- Cerebellum

Hi Sabin, I think fslmeants should work. But you might need to first run mri_binarize to convert Buckner_atlas_FSSub.nii.gz into individual ROIs. Also can you tell us which step generated the error "ERROR: must specify a segmentation volume"? Is this the final step? Have you tried overlaying

Re: [Freesurfer] FSFAST- Cerebellum

Hi Thomas- On second thought is it valid to simply do if I want average time series of the cerebellum regions? fslmeants -i fmcpr.anat.nii.gz -m Buckner_atlas_FSSub.nii.gz >> avgCerebellum.txt Is this correct? Cheers, Sabin Khadka On Mon, Jun 27, 2016 at 11:36 AM, Sabin Khadka

Re: [Freesurfer] FSFAST- Cerebellum

Hi Thomas and Doug- Thanks for you suggestions. Per your suggestions I performed following recon-all -i $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/FSL_MNI152_FreeSurferConformed_1mm.nii.gz -subjid Yeo2011_MNI152_FS recon-all -no-isrunning -autorecon-all -subjid Yeo2011_MNI152_FS

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