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 contras

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 r

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 resti

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? - do

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 PM,

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 yo

Re: [Freesurfer] FSFAST first level covariates

:angf...@uw.edu> Reply-To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, August 1, 2022 at 4:35 PM To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FSFAST first level covariates External Email -

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

: 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 ar

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 mkcontrast

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 - Us

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 analy

Re: [Freesurfer] fsfast no run directories

In the bold directory, it looks like you have one run directory called "1". Change this to "001" On 11/29/2019 1:48 AM, Renew Andrade wrote: External Email - Use Caution Dear FreeSurfer experts: I have some issues with "preproc-sess" because I cannot seem to get the setup of the direct

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 */bold/audio.lh/tones/c

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 o

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 n

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 di

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 t

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. Tha

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 Wo

Re: [Freesurfer] FSFAST poor registration

External Email - Use Caution Hi Douglas Thank you for your reply. I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a I am using whole brain data. The functional and structural images were acquired in different sessions on the same day, I don't know if that compl

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 simila

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

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 localize

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 for your previous answer.

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 only

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 middle

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 a presented stimuli? > Sa

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 wrote: > That file s

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 with

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 performin

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 L_Posteriorcingulat

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 by

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 s

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 volum

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 f

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

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 ther

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 g

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). -

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 comput

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 there

Re: [Freesurfer] FSFAST ROI atlas

ychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: Sabin Khadka > Date: Wednesday, August 17, 2016 at 11:25 AM > To: Freesurfer support list , "Harms, > Michael" > > Subject: Re: [Freesurfer] FSFA

Re: [Freesurfer] FSFAST ROI atlas

rtment of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: on behalf of Doug Greve < > gr...@nmr.mgh.harvard.edu> > Reply-To: "freesurfer@nmr.mgh.harvard.edu" > > Date: Wednesday, August 17,

Re: [Freesurfer] FSFAST ROI atlas

alf 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 ho

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 AM, Sabin Khadka wrote: > > H

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

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

/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin Sorry if my response seems naïve, I’am new to running command lines although I’m trying learn. Erik Message: 6 Date: Fri, 8 Jul 2016 14:30:43 -0400 From: Douglas N Greve <mailto:gr...@nmr.mgh.harvard.edu>> Subject: Re: [Free

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 walkthro

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 spa

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 > -fwh

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 Buck

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 wrote: > Hi Th

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 mri_vo

Re: [Freesurfer] FSFAST- Cerebellum

Hi Doug, thanks. Hi Sabin, you can use the following steps to transform the Buckner cerebellum atlas to your subject's native anatomical space and then follow Doug's instructions (taken and adapted from another user Bronwyn's email): 1. Run MNI152 1mm template through recon-all recon-all -i FSL_M

Re: [Freesurfer] FSFAST- Cerebellum

yes On 6/24/16 9:19 AM, Thomas Yeo wrote: > Hi Doug, > > Would your mri_segstats command work if instead of aseg.mgz, Sabin > passed in the cerbellum parcellation in the same anatomical space as > aseg? > > --Thomas > > On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve > wrote: >> After you run pr

Re: [Freesurfer] FSFAST- Cerebellum

Hi Doug, Would your mri_segstats command work if instead of aseg.mgz, Sabin passed in the cerbellum parcellation in the same anatomical space as aseg? --Thomas On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve wrote: > After you run preproc-sess, there will be a file called register.dof6.dat. > M

Re: [Freesurfer] FSFAST- Cerebellum

After you run preproc-sess, there will be a file called register.dof6.dat. Map fmri into the anatomical space, something like mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o fmcpr.anat.nii.gz Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz However, I don't

Re: [Freesurfer] FSFAST- Cerebellum

Hi Yeo- Thanks very much for your answer. Yes the data is in mni305 space. I process my fmri data with preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 -per-run -stc odd and then to extract ROI time series values I did mri_segstats --annot fsaverage rh aparc --i rest210/b

Re: [Freesurfer] FSFAST- Cerebellum

Hi Sabin, The structures 601-628 FreeSurferCololLUT.txt correspond to anatomical substructures of the cerebellum (e.g., Crus I, etc). Is that what you want? Or are you looking to use the functional parcels defined in Buckner 2011? In addition, I do not know how mri_segstats works, so I cannot ver

Re: [Freesurfer] FSFAST (seed based correlation analysis)

you could use fsfast to do it, but it might be doing some things you dont want. Eg, high-pass smoothing. PET images are usually acquired over hours and the high-pass filtering may remove stuff you want. Also, PET images are usually not spaced uniformly in time (should not matter if you're just

Re: [Freesurfer] FSFAST with reoriented reconstruction

In general, FreeSurfer does not care what orientation your images are in as long as the geometry in the header file is correct. If you re-oriented them for SPM and you are confident that the geometry info is still correct (eg, no left-right flips) and you did not change the scale of the images

Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question

On 03/24/2016 07:37 PM, Joseph Dien wrote: > Doug, I see now what your concern was with just adjusting the beta > weights. Since FSFAST is using a pseudo-mixed effects model, there is > also a need to pass the cesvar statistics up to the second level. How > that might accommodate the derivat

Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question

Doug, I see now what your concern was with just adjusting the beta weights. Since FSFAST is using a pseudo-mixed effects model, there is also a need to pass the cesvar statistics up to the second level. How that might accommodate the derivative boost computation is not straightforward to me.

Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question

I did more digging around and came up with a procedure. Please let me know if it would cause any problems. Looking at the contents of the X.mat files (which contain the predictors), it appears that the betas are indeed arranged as c1 d1 c2 d2… I also found that isxconcat-sess requires the contra

Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question

oh duh! Sorry, wasn’t thinking clearly. Okay, I see how to generate the betas now. I don’t even need to mess with the mkcontrast-sess command. I just run selxavg3-sess with the -no-con-ok flag. With spmhrf 0 I generated a beta.nii.gz file with 85 betas in each vertex. With spmhrf 1 I generated a

Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question

The setwdelay is an option for mkcontrast-sess (not mkanalysis-sess) On 03/13/2016 10:29 PM, Joseph Dien wrote: > After a long break, back to this… > > My goal is still to get the betas for the first and maybe second spm > hrf so I can calculate a Calhoun derivative boost measure. > > As a first

Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question

After a long break, back to this… My goal is still to get the betas for the first and maybe second spm hrf so I can calculate a Calhoun derivative boost measure. As a first step I ran: mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm RPA1f

Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR

vard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana > [aaf...@mgh.harvard.edu] > Sent: Monday, November 16, 2015 2:14 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERRO

Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR

-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana [aaf...@mgh.harvard.edu] Sent: Monday, November 16, 2015 2:14 PM To: Freesurfer support list Subject: Re: [Freesurfer] FSFAST First

Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR

u] on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu] > *Sent:* Friday, November 13, 2015 5:04 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR > > hmmm, not sure. Can you send me your selxavg3-sess command

Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR

r.mgh.harvard.edu] > *Sent:* Friday, November 13, 2015 5:04 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR > > hmmm, not sure. Can you send me your selxavg3-sess command and the > folder your ran it from and the

Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR

ubject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR hmmm, not sure. Can you send me your selxavg3-sess command and the folder your ran it from and the $SUBJECTS_DIR ? doug On 11/13/15 4:16 PM, Afzal, Afsana wrote: Hi, I'm doing first level analysis in FSFAST and I'm cons

Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR

hmmm, not sure. Can you send me your selxavg3-sess command and the folder your ran it from and the $SUBJECTS_DIR ? doug On 11/13/15 4:16 PM, Afzal, Afsana wrote: Hi, I'm doing first level analysis in FSFAST and I'm consistently getting the following error when running fast_selxavg3(): Savin

Re: [Freesurfer] FSFAST -per-run question

Just that the middle would be expected to have the least amount of motion with the rest of the run and so result in less interpolation On 10/22/2015 05:15 PM, dgw wrote: > Hi, > > I know that -per-run is the recommended motion correction option, and > that it uses the middle frame as the referenc

Re: [Freesurfer] FSFAST

you can, but not from preproc-sess. This is controlled by mktemplate-sess which is called from preproc-sess, but you can run it separately. Specify the frame you want with -frame and run it with -force to force it to overwrite the other results. Then run preproc-sess (but not with -force !) and

Re: [Freesurfer] fsFast by Octave - minor problems

Thanks Antonin, I've incorporated the rho1 change into fast_selxavg3.m. Was there a change that would fix the parfile problem? On 03/04/2015 08:00 AM, Antonin Skoch wrote: > Dear Freesurfer experts, > > I run fsFast by Octave and I came across minor problems, which are > specific to Octave, to

Re: [Freesurfer] FSFAST

On 2/18/15 4:38 PM, sabin khadka wrote: Hi FS Users- After using FSFAST's preproc-sess command (I get the output files: fmcpr.up.sm5.fsaverage.lh.nii.gz,fmcpr.up.sm5.fsaverage.rh.nii.gz, fmcpr.up.sm5.mni305.nii.gz), I was wondering if we could see or tell how well the EPIs are mapping onto th

Re: [Freesurfer] fsfast: using an empirically derived HRF with mkanalysis-sess

On 9/14/14 1:55 PM, Alex Kell wrote: hi freesurfers, i would like to use an empirically derived HRF with mkanalysis-sess. i have derived the HRF i want [via an FIR model], but it's not obvious how i can use my custom HRF with mkanalysis-sess. one option, it seems, is to feed in my own regr

Re: [Freesurfer] fsfast: using an empirically derived HRF with mkanalysis-sess

and one point of clarification: i only care about beta weights for each condition of interest, so i don't care that -taskreg would only run an F-test for significance maps and wouldn't give me t maps for each regressor of interest. thanks again, alex On Sun, Sep 14, 2014 at 1:55 PM, Alex Kell w

Re: [Freesurfer] FsFast Functional Connectivity Analysis

Hi Doug, My issue is I am not intending to use a labeled segmented ROI. My main goal is to calculate the connectivity strength between two binarized ROIs that are functionally defined. Can fcseed-config accept non Freesurfer segmented ROIs? Thanks, JIahe On Fri, Sep 12, 2014 at 11:08 AM, Douglas

Re: [Freesurfer] FsFast Functional Connectivity Analysis

You need to have your ROI as a segmentation in the anatomical (conformed) space. If it is a label on the surface, you can use mri_label2vol to turn it into a volume (make sure to use --proj frac 0 1 .1 to fill the ribbon). When you run funcroi-config specify -seg yourseg.mgz 1 where yourseg.m

Re: [Freesurfer] FsFast Functional Connectivity Analysis

Hi Doug, I was able to get the surface connectivity analysis to run successfully for the L.Cingulate example that you posted online ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough ). For my own analysis, I'm hoping to use my own functionally defined ROIs instead

Re: [Freesurfer] FsFast Functional Connectivity Analysis

How did you look at fmcpr.up.sm6.fsaverage.lh.nii.gz? If you did not do this, try it tksurfer fsaverage lh inflated -ov fmcpr.up.sm6.fsaverage.lh.nii.gz -t fmcpr.up.sm6.fsaverage.lh.nii.gz This will bring up an overlay as well as a time course On 08/11/2014 05:05 PM, Jiahe Zhang wrote: > Both

Re: [Freesurfer] FsFast Functional Connectivity Analysis

Both looked fine. First value in .mincost is .45 On Mon, Aug 11, 2014 at 4:51 PM, Douglas N Greve wrote: > two ways: > > 1. run tkregister-sess to visually check them > 2. look at the first value in register.dof6.dat.mincost. It is hard to > say what a threshold is for a good registration, but

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