Re: [Freesurfer] How to deal with the distortions of EPI images when applying the parcellated results of T1 images?

Thanks a lot for your prompt reply, Doug and Bruce. I did collect field maps and just tried epidewarp.fsl, but I met with the following error "FSL Version is 5.0.6, must be 3.X or 4.X". I've searched the email archives and found a message about epidewarp.fsl that works with FSL 5 from Doug, howeve

Re: [Freesurfer] How to deal with labels and structural data

Hi Bruce, I would like to make a ROI analysis where i'll investigate cortical thickness of the labels - and afterwards use the labels to make a ROI analysis of fMRI data and t1t2ratio data which is mapped onto the fsaverage (I've already made an analysis "on the surface"). My question is how to

Re: [Freesurfer] paradigm file

Each entry in the paradigm file represents a presentation characterized by 4 values: 1. Onset time 2. Stimulus code (integer 0-N) 3. Stimulus duration 4. Weight (usually 1) If each stimulus presentation has a different duration, then that would be indicated in #3 doug On 7/22/15 12:23 AM, Th

Re: [Freesurfer] How to deal with the distortions of EPI images when applying the parcellated results of T1 images?

Try using this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl On 7/22/15 4:03 AM, Bingjiang Lyu wrote: Thanks a lot for your prompt reply, Doug and Bruce. I did collect field maps and just tried epidewarp.fsl, but I met with the following error "FSL Version

Re: [Freesurfer] mri_convert command line did not provide output file

Hi Stefano can you send us the command that was run and the full output? Bruce On Wed, 22 Jul 2015, std...@virgilio.it wrote: > Hi list, > > mri_convert command line did not provide output file. > > This error was produced during the first computations of trac-all -prep > command line. > >

Re: [Freesurfer] How to deal with labels and structural data

Hi Silas I think we already provide the information you want as we tabulate the thickness of the different parcels in the various files in each subject's stats dir. If you want to do the same thing with a different set of labels draw the labels on fsaverage, use mri_label2label to map them to

Re: [Freesurfer] QDEC question

The statements are automatically generated based on the names of the variables you provide. In this case, you've included (global?) lh thickness as a covariate. This will have a slope when plotted against thickness at a given vertex, and this slope my differ between genders. The "average" th

[Freesurfer] R: Re: mri_convert command line did not provide output file

Thanks Here is attached. INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_provaINFO: Diffusion root is /Applications/freesurfer/subjects/subject_provaActual FREESURFER_HOME /Applications/freesurfertrac-preproc -c $SUBJECTS/Control75/scripts/dmrirc.local -log $SUBJECTS/Control75/s

Re: [Freesurfer] R: Re: R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

The commands look ok. On 7/21/15 8:26 PM, std...@virgilio.it wrote: My concern is whether this command line is correct fcseed-config -segid 1 -seg ROI_MASK. -fsd rest -mean -cfg mean.ROI_MASK.config fcseed-sess -s SessXXX -cfg mean.ROI_MASK.config Thank you Stefano Messaggio originale

[Freesurfer] cluster_wise correction

Hello Freesurfer Experts I have got the statistic P map ( -log10(p)),such as the 'Patient-smaller-Control_P_on_fsaverage4_lh.mgh', now i want to do the cluster_wise correction with p<0.05., or do the FDR correction. Could you please give me some suggestions how to do it? Thank you very much!

Re: [Freesurfer] Dividing Entire Scan By Intensity Factor & Create Overlay Surface

(I apologize in advance if I have not used the reply correctly and have accidentally started a new thread - still new to this board!) I thought it might help if I laid out all of my steps and code to reach the part where I am having problems. I am attempting to use the longitudinal pipeline ou

[Freesurfer] Subcortical segmentation necessary steps

Dear Freesurfer Team, I am inquiring as to what are the necessary steps to run in recon all if one only wants to perform subcortical segmentation and relevant statistics. I just want to run the necessary steps for these to run properly. Thanks so much for your help. TK __

Re: [Freesurfer] Subcortical segmentation necessary steps

Hi Tony if you run recon-all it will do everything needed. You could stop after mri_ca_label I suppose, but then you won't be able to use the surfaces to correct white matter and cortex. cheers Bruec On Wed, 22 Jul 2015, Tony Koroulakis wrote: > Dear Freesurfer Team, > > I am inquiring as t

Re: [Freesurfer] if: Expression Syntax

Hi there, I’m running stable: source /usr/local/freesurfer/stable5_3_0 Thanks, Keji > On Jul 21, 2015, at 4:56 PM, Douglas Greve wrote: > > what environment are you running in? ie, dev or stable? > > On 7/21/15 2:12 PM, Morenikeji Adebayo wrote: >> Hi there, >> >> When running selxavg for t

Re: [Freesurfer] help with using optseq2

Thank you for the reply. I am ended up using afni's make_random_timing.py to solve the problem. Best, Heeyoung From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] S

Re: [Freesurfer] help with using optseq2

Thank you for the reply. I am ended up using afni's make_random_timing.py to solve the problem. Best, Heeyoung From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of MCLAREN, Donald [mclaren.don...@gmail.com] S

Re: [Freesurfer] if: Expression Syntax

* Can you run the following preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.log and send me fordoug.log On 07/22/2015 02:12 PM, Morenikeji Adebayo wrote: > Hi there, > > I’m running stable: > > source /usr/local/freesurfe

[Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model

Dear Freesurfers, I am trying to use the longitudinal 2-stage model to run a mri_glmfit analysis. How do I specify my FSGD file so that I compared spc or pc1 maps instead of the regular thickness maps? Also, it is my understanding that I do not have to run mris_preproc and mri_surf2su

Re: [Freesurfer] if: Expression Syntax

Hi Doug, When I run: preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.log I get: preproc-sess: No match. Thanks, Keji > On Jul 22, 2015, at 3:37 PM, Douglas N Greve > wrote: > > * > Can you run the following > > prepro

Re: [Freesurfer] if: Expression Syntax

Sorry, there should not be a * at the end of -per. I was just trying to copy your command line with -debug as the first arg. On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote: > Hi Doug, > > When I run: > preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface > fsaverage lhrh -min305

Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model

Hi Koushik, the output of the long_mris_slopes will be (by default) in each subjects base/template directory, so you would have to map things to, e.g. fsaverage and stack +smooth everythibng before running mri_glmfit. You can also make use of the long_mris_slope flags --stack-spc and --qcac

Re: [Freesurfer] if: Expression Syntax

No problem! Here you go. fordoug.log.docx Description: MS-Word 2007 document On Jul 22, 2015, at 4:30 PM, Douglas N Greve wrote:Sorry, there should not be a * at the end of -per. I was just trying to copy your command line with -debug as the first arg.On 07/22/2015 04:0

Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed}

Thanks for the detailed reply Martin. When you say "here we mean really subjects, not time points, as there is only one SPC map per subject", are you referring to the base template name? Also, as an extension to my previous question, if I have 3 timepoints (tp1, tp2 and tp3). Is it possible for

Re: [Freesurfer] if: Expression Syntax

can you just send the log and not put it into a doc file? On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote: > No problem! Here you go. > > > >> On Jul 22, 2015, at 4:30 PM, Douglas N Greve >> mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> Sorry, there should not be a * at the end of -per. I was

Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed}

Yes, I mean the base name, but not repeated (so only lilsted once per base), so you cannot simply copy that column from the long qdec file. The PC1 is the slope of the linear fit with respect to the first time point (the SPC with respect to the value of the linear fit at the mid time point and

Re: [Freesurfer] if: Expression Syntax

I sure can. Hopefully. Is the what you need? fordoug.log Description: Binary data On Jul 22, 2015, at 5:01 PM, Douglas N Greve wrote:can you just send the log and not put it into a doc file?On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote:No problem! Here you go.On Jul

Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed}

Thanks again Martin. tp1 is really my baseline and so I want to compare the rate of change from baseline to tp2 and tp3. So, I think the 1st option would not work. If I do use the longitudinal 2 stage model and then mri_glmfit, I would have 2 stacked files (1 for each comparison) and also, insi

[Freesurfer] Problems with longitudinal processing

Hi, I am running longitudinal processing with Freesurfer according to the instructions on freesurfer website here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics So in step2, I ran recon-all -base template -tp subPRE/subPRE/mri/norm.mgz -tp subPOST/subPOST/mri/norm.mgz -sd /home

Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed}

Hi Koushik, If that is what you want to do, the first option works: (tp2-tp1) - (tp3-tp1) = tp2 - tp3 Best, Martin On 07/22/2015 06:25 PM, Govindarajan, Koushik Athreya wrote: > Thanks again Martin. tp1 is really my baseline and so I want to compare the > rate of change from baseline to tp2 and

Re: [Freesurfer] Problems with longitudinal processing

Hi Diane, for -tp you need to pass the id of the processed time points from the first step. So if you have two time points and called the subject ids subPRE and subPOST then recon-all -base subTemplate -tp subPRE -tp subPost -sd Both the subPRE and the subPost need to be in the same subject

Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed}

Thanks Martin. I will try that. Regards Koushik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: Wednesday, July 22, 2015 6:48 PM To: Freesurfer support l