[Freesurfer] mri_glmfit problem/2 group 6 covariates

Hello doug, while running the mir_glmfit problem, i encountered this problem “ INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 39.9375 17.3312 1 Education 15.5625 1.99902 2 Firstscore 1.03375 0.341785 3 Secondscore 1.03906 0.3706

[Freesurfer] normalizing in fsgd

Hello freesurfer experts, I am trying to normalize my continuous variables in my fsgd file. Is this the correct term to add to my fsgd file in order for mri_glmfit to normalize it? GroupDescriptorFile 1 Title PCS Class group1 Class group2 Normalize 1 Variables Age Education Scoreone Scoretwo Input

Re: [Freesurfer] mri_glmfit problem/2 group 6 covariates

wrote: > Try demeaning and normalizing your continuous covariates in the FSGD file. > > On 07/22/2016 06:17 PM, miracle ozzoude wrote: > > > > Hello doug, > > > > while running the mir_glmfit problem, i encountered this problem “ > > > > INFO: DeMean

Re: [Freesurfer] mri_glmfit problem/2 group 6 covariates

, 2016 at 11:19 AM, Douglas Greve wrote: > Can you send your new fsgd file and new design matrix? > > On 7/24/16 6:06 PM, miracle ozzoude wrote: > > Hello Doug or Bruce, > I demeaned and normalize like you suggested but I'm still getting the same > results. I created a new fs

Re: [Freesurfer] normalizing in fsgd

gt; > in addition to > > DeMeanFlag 1 > > > > > On 7/25/16 11:22 AM, Douglas Greve wrote: > > No, that flag does not exist, but it is a good idea! You'll have to > normalize them by hand. > > On 7/24/16 1:33 PM, miracle ozzoude wrote: > > Hello freesurfer

Re: [Freesurfer] normalizing in fsgd

file (if using one) 3. And the design matrix above On Tue, Jul 26, 2016 at 12:23 PM, Douglas N Greve wrote: > what do you mean it did not work? can you be more specific? > > > On 07/26/2016 12:21 PM, miracle ozzoude wrote: > > Hello Doug, > > The ReScaleFlag 1 comman

Re: [Freesurfer] mri_glmfit problem/2 group 6 covariates

las N Greve wrote: > Can you resend the design matrix? > > On 07/26/2016 11:46 AM, miracle ozzoude wrote: > > Hello Doug, > > Sure. Here are my new fsgd file and new contrast matrix ( matrix is > > the same as the old one). > > Best, > > Paul > > Gr

[Freesurfer] group analysis/ region of interest (ROI) approach

Hey FreeSurfer experts, Does anyone know the steps i have to perform if I want to conduct surface based thickness analysis using GLM but with ROI approach. Thank you very much. Best, Paul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://

Re: [Freesurfer] group analysis/ region of interest (ROI) approach

> > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI > > After you run aparcstats2table, you can run mri_glmfit with --table > aparcstatstable instead of --y. The output folder will have tables with > lists of ROIs and p-values > > > > On 7/30/16 5

[Freesurfer] mri_label2label

Hello, i used mri_annotation2label to extract individual parcellations for my subjects. Do I need to register my subjects to fsaverage using mri_label2label before creating a mask for ROI surface based analysis using GLM dods? Thanks Best, Paul ___ Frees

[Freesurfer] mri_glmfit-sim problem

Hello FreeSurfer experts, I am running surfaced based analysis using ROI approach. My mris_preproc, mri_surf2surf and mri_glmfit worked as expected. Since i restricted the region i built my own monte carlo "mri_mcsim --o roianalysis/average/mult-comp-cor/fsaverage/rh/rightmaskforcomp --base mc-z --

Re: [Freesurfer] mri_glmfit-sim problem

Hello, Never mind. I was able to figure it out. I only needed to add "Users/Paul/Desktop" to the command line On Wed, Aug 10, 2016 at 12:50 PM, miracle ozzoude wrote: > Hello FreeSurfer experts, > I am running surfaced based analysis using ROI approach. My mris_preproc, >

[Freesurfer] malloc_error_break/ can't allocate region

Hello FreeSurfer team, While running monte carlo correction with 1 reps (mri_mcsim) for the whole hemisphere, I received this error at 975 reps for the left hemisphere " 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216) failed (error code=12) *** error: can't allocate region *** set

Re: [Freesurfer] malloc_error_break/ can't allocate region

FS 5.1.0. I tried it with 5000 reps for ROI analysis and it worked. On Tue, Aug 16, 2016 at 3:46 PM, Douglas N Greve wrote: > What version of FS (and mri_mcsim) are you using? Does it die if you run > with just a few reps (eg, 100)? > > On 08/16/2016 01:21 PM, miracle ozzoude wrot

[Freesurfer] recon-all/ mri_convert (preprocessing dicom file error)

Hello, I am trying to preprocess couple of dicom images (146 dicom image) and I constantly get this error. "dan% *recon-all -all -i IM-0065-0001.dcm -s fsdir (recon-all script)* Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO:

[Freesurfer] monte carlo continue/ desktop restarted

Hello experts, I was running 1 monte carlo simulation before my desktop automatically restarted, does anyone know a command to continue from where it stopped? The simulation for left hemisphere stopped at 9146/1 and right hemisphere at 9125/1. Thank you Paul

Re: [Freesurfer] monte carlo continue/ desktop restarted

Thank you Doug Paul On Wed, Sep 28, 2016 at 10:39 AM, Douglas N Greve wrote: > I would just use what was created. There is nothing magical about 10,000 > iterations. A few iterations short won't make any difference. > > > On 09/28/2016 10:35 AM, miracle ozzoude wrote: >

Re: [Freesurfer] monte carlo continue/ desktop restarted

bject/rh/cortex \ --base mc-z --surface yoursubject rh --nreps 1 On Wed, Sep 28, 2016 at 10:39 AM, Douglas N Greve wrote: > I would just use what was created. There is nothing magical about 10,000 > iterations. A few iterations short won't make any difference. > > > On 0

Re: [Freesurfer] monte carlo continue/ desktop restarted

Thank you On Wed, Sep 28, 2016 at 3:49 PM, Douglas Greve wrote: > There is no way. Yes, you can specify fsaverage for yoursubject > > On 9/28/16 3:47 PM, miracle ozzoude wrote: > > Hello Doug, > Do you know if there's any command to make it continue from where it >

[Freesurfer] GLM on cortical and subcortical volume

Hello Expert, Is there are way to perform glm analysis on cortical and subcortical volumes. Thanks Best,. Paul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in thi

Re: [Freesurfer] GLM on cortical and subcortical volume

OIs? Yes, there is a tutorial on this in our wiki, > but basically you need to run aparcstats2table and/or asegstats2table to > create a table of volumes for each subject and ROI. Then use mrI_glmfit > with the --table option instead of --y > > On 10/18/16 10:18 AM, miracle ozzoude wrote

[Freesurfer] adding control points and pial editing

Hello Freesurfer, I have 100 participants for my study and I would like to add control points and edit the pial for all of them. Is there a command that can automatically do both or do I have to manually inspect all 100 participants and add control point/ pial edit where necessary. thanks. Best, Pa

[Freesurfer] skull stripping and white matter labelling

Hello experts, I did my skull stripping and white matter labelling using an lesion explorer and I want to replace the brainmask.mgz and wm.seg.mgz generated by freesurfer with the brainmask and wm.seg.mz from lesion explorer. Is there a freesurfer script that can do it? Thanks, Paul __

[Freesurfer] difficulty opening fsdir on freesurfer linux

Hello Freesurfer team, I am having difficulty opening the fsdir folder on freesurfer linux version (linux-centos_x86_64-stable-pub-v5.3.0). First, I preprocessed it using the command "recon-all -all -i s fsdir" to get the fsdir folder and it finished without errors. However, when I tried loading th

[Freesurfer] recon-all steps question

Hello Freesurfer, I have couple of questions. While going through the frequently asked questions on your page http://freesurfer.net/fswiki/UserContributions/FAQ I came across a question regarding how to integrate a skull stripped from another problem into freesurfer (using recon-all -autorecon1 -no

Re: [Freesurfer] recon-all -autorecon2 error.

the > orig.mgz? You may need to conform you brainmask > > > On Mon, 28 Nov 2016, miracle ozzoude wrote: > > Hello Freesurfer, I ran recon-all -autorecon 1 -s subjID on T1 (T1_nii) >> image and after >> that, I replaced the skull stripped volume generated from FS with the

Re: [Freesurfer] recon-all -autorecon2 error.

rer after i have renamed it to brainmask.mgz). Also, I didn't use the "noskullstrip" flag like you suggested. Best, paul On Mon, Nov 28, 2016 at 3:50 PM, Bruce Fischl wrote: > I mean after you have converted it > > On Mon, 28 Nov 2016, miracle ozzoude wrote: > > Thanks

Re: [Freesurfer] recon-all -autorecon2 error.

ers > Bruce > On Mon, 28 Nov 2016, miracle ozzoude wrote: > > This was the info from mri_convert when i converted my skull stripped >> volume to mgz >> before replacing it with the brainmask from FS >> mri_convert --in_type analyze --in_orientation LAS --out_

Re: [Freesurfer] recon-all -autorecon2 error.

gt; > coords as the other volumes. YOu probably need to -rl orig.mgz in your > > conversion, then make sure that the volumes look aligned in freeview (and > > that mri_info gives the same ras2vox and such for them) > > On Mon, 28 Nov 2016, > > miracle ozzoude wrote: > &

Re: [Freesurfer] recon-all -autorecon2 error.

PM, Bruce Fischl wrote: > > you may not need the out_orientation, but perhaps someone else knows? > > On Tue, 29 Nov 2016, miracle ozzoude wrote: > > > >> Hello Bruce, > >> I wanted to confirm if this is the right script when converting from > >

Re: [Freesurfer] recon-all -autorecon2 error.

hp Please can you inspect to see why both images (orig.mgz and brainmask.mgz) do not align and cannot finish recon-all -autorecon2? THANK YOU VERY MUCH Paul On Tue, Nov 29, 2016 at 3:20 PM, miracle ozzoude wrote: > Hello Doug and Bruce, > > I ran the script and it worked however, vo

[Freesurfer] Fwd: Edit to wm.seg.mgz.

-- Forwarded message -- From: Date: Fri, Dec 2, 2016 at 5:42 PM Subject: Edit to wm.seg.mgz. To: Freesurfer support list Hello Freesurfer, I replaced wm.seg.mgz from freesurfer with white matter +lesion (called it wm.seg.mgz before replacing) from lesion explorer. Do I run recon

Re: [Freesurfer] Fwd: Edit to wm.seg.mgz.

cheers > Bruce > > > > On Mon, 5 Dec 2016, miracle ozzoude wrote: > > >> -- Forwarded message -- >> From: >> Date: Fri, Dec 2, 2016 at 5:42 PM >> Subject: Edit to wm.seg.mgz. >> To: Freesurfer support list >> >> &

[Freesurfer] under estimation of white matter and pial surface

Hello Freesurfer, I was wondering if anyone knows how to correct an underestimation of white matter and pial surface outputs from freesurfer. I attached an image showing the error. Thanks. Best, Paul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.

[Freesurfer] Fwd: under estimation of white matter and pial surface

-- Forwarded message -- From: miracle ozzoude Date: Wed, Dec 28, 2016 at 2:53 PM Subject: under estimation of white matter and pial surface To: Douglas N Greve Hello Freesurfer, I was wondering if anyone knows how to correct an underestimation of white matter and pial surface

Re: [Freesurfer] under estimation of white matter and pial surface

ce > > On Wed, 28 Dec 2016, miracle ozzoude wrote: > > Hello Freesurfer, I was wondering if anyone knows how to correct an >> underestimation of white matter and pial surface outputs from freesurfer. >> I >> attac

Re: [Freesurfer] under estimation of white matter and pial surface

can I use Martinos center because I am not familiar with ftp? Thanks On Thu, Dec 29, 2016 at 2:07 PM, Bruce Fischl wrote: > https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange > > On Thu, 29 Dec 2016, miracle ozzoude wrote: > > Thanks bruce. How do I upload the subjec

Re: [Freesurfer] under estimation of white matter and pial surface

I have sent it. Thanks Bruce. Best, Paul On Thu, Dec 29, 2016 at 2:07 PM, Bruce Fischl wrote: > https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange > > On Thu, 29 Dec 2016, miracle ozzoude wrote: > > Thanks bruce. How do I upload the subject?Best, >> Paul >> &

[Freesurfer] recon-all in stages with T2pial

Hello Freesurfer, I was trying to run recon-all in stages (autorecon1, autorecon-2 and autorecon3) with T2. First, I ran autorecon1 with T2 (recon-all -autorecon1 -i input_volume -T2 /T2_volume -T2pial -s ) and i got an error (MRISread (./surf/lh.white): could not open file Loading mov Pro

[Freesurfer] mris_make_surfaces scripts and how and when to use

Hello Freesurfer, I was going to the ReconAllDevTable ( https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) and i came across 3 different mris_make_surfaces scripts. 1) When do I use any of the 3 mris_make_surfaces scripts after running recon-all -all? 2) Is there a default/standard nsigma

[Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

-- Forwarded message -- From: miracle ozzoude Date: Mon, Jan 9, 2017 at 11:06 AM Subject: mris_make_surfaces scripts and how and when to use To: Douglas N Greve Hello Freesurfer, I was going to the ReconAllDevTable (https://surfer.nmr.mgh. harvard.edu/fswiki/ReconAllDevTable

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

looks right to me > > cheers > Bruce > > On Mon, 9 Jan 2017, miracle ozzoude wrote: > > >> -- Forwarded message -- >> From: miracle ozzoude >> Date: Mon, Jan 9, 2017 at 11:06 AM >> Subject: mris_make_surfaces scripts and how and when to use

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

low, which is what my response > referred to > > > On Mon, 9 Jan 2017, miracle ozzoude wrote: > > Thanks bruce for your response. Please, which of my questions did you >> answer since I listed 4. Best, >> Miracle >> >> On Mon, Jan 9, 2017 at 2:46 PM, Bruce Fis

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

> > I think this problem is fixed in 6.0 (if and when we get it out) > > On Mon, 9 Jan 2017, miracle ozzoude wrote: > > > Thanks bruce for your response. I accidentally listed number 3 twice instead > of 4. Here's my 4th question: Which of the mris_make_surfaces can

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

9, 2017 at 4:19 PM, miracle ozzoude wrote: > Thanks a lot Antonin.I will try it out. I am trying to figure out how to > use mris_make_surfaces to extend my pial surface with T2 argument included > and also, play around with -first_wm_peak and -nsigmas > > On Mon, Jan 9, 2017 at

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

t; the gray/white boundary isn't as big a jump in contrast as > infragranular/supragranular. It usually is only needed for hires data > > cheers > Bruce > > On Mon, 9 Jan 2017, miracle ozzoude wrote: > > hello Bruce, I have another question, what's the function of -firs

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

another question. How do I incoporate -cover_seg into it? do i need surfaceRAS coordinates for the seg? Thanks, Best Paul On Mon, Jan 9, 2017 at 5:04 PM, miracle ozzoude wrote: > Thanks for your response bruce. Do you think I can use it for 3T scans and > do i need to specify a sp

[Freesurfer] reposition surface for pial surface

Hello Freesurfer, I would like to learn how to use the reposition surface tool in freeview. Specifically, what parameters to enter in the gui (see screenshots). Is there any documentation on how to use it if not, can someone with experience work me through it. Thank you. best, Paul

Re: [Freesurfer] reposition surface for pial surface

. Thanks Best, Paul On Tue, Jan 10, 2017 at 12:42 PM, Bruce Fischl wrote: > Hi Paul > > sorry, this is something that Ruopeng put together for me to mess around > with - there isn't any documentation > > cheers > Bruce > > On Tue, 10 Jan 2017, miracle ozzoude wrote: &g

Re: [Freesurfer] reposition surface for pial surface

ail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-October/026117.html). > Use = directions and parameters to input. Thanks > Best, > Paul > > On Tue, Jan 10, 2017 at 12:42 PM, Bruce Fischl > wrote: > > > Hi Paul > > > > sorry, this is something that Ruopeng pu

Re: [Freesurfer] reposition surface for pial surface

or example here > > > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg37990.html > > > > > could help you to get satisfactory results (however, the altering of these > > parameters should be done in my opinion for all subjects in the study to > &

[Freesurfer] mris_expand command and flags

Hello freesurfer, I have several questions about mris_expand command. I know it can be used to expand or shrink a point on a surface by a fixed amount or distance. My questions are: 1) Can it be used to expand the pial surface? if yes, please can you confirm if this is the right script= mris_expan

Re: [Freesurfer] mris_expand command and flags

hard to answer your questions without knowing what you are trying to > achieve > > cheers > Bruce > > On Wed, 11 Jan 2017, miracle ozzoude wrote: > > Hello freesurfer, >> I have several questions about mris_expand command. I know it can be used >> to expand o

Re: [Freesurfer] mris_expand command and flags

uce Fischl > wrote: > > > Hi Paul > > > > it's hard to answer your questions without knowing what you are trying to > > achieve > > > > cheers > > Bruce > > > > On Wed, 11 Jan 2017, miracle ozzoude wrote: > > > > Hello freesurf

[Freesurfer] volume based GLM group analysis(whole brain and ROI).

Hello Freesurfer, I would like to do a GLM volume based analysis using the cortical volumes from desikan atlas (structural not functional). However, I can't find the steps/tutorials on how to do this on the freesurfer website. Does anyone know how to do this using freesurfer? Basically, I want to p

[Freesurfer] whole hemisphere is yellow

hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle ___ Freesurfer mailing list Freesurfer@nmr.

Re: [Freesurfer] whole hemisphere is yellow

: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow Hi Miracle have you tried changing the thresholds? What kinds of values are you seeing? Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote: > hello doug, > i performed a group analysis and

Re: [Freesurfer] whole hemisphere is yellow

: [Freesurfer] whole hemisphere is yellow if it's all yellow it means everything is significant. What threshold are you using? On Thu, 24 Mar 2016, Miracle Ozzoude wrote: > Hello Bruce, > No. This was after I ran the correction for multiple comparisons. Do I need > to change the threshold

Re: [Freesurfer] whole hemisphere is yellow

of Douglas N Greve Sent: March 24, 2016 6:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow Can you give us more info about the design and the contrast you are testing? What does the uncorrected map look like? On 03/24/2016 09:56 AM, Miracle Ozzoude

Re: [Freesurfer] whole hemisphere is yellow

mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos --cwpvalthresh 0.05 --2spaces From: Douglas N Greve Sent: March 25, 2016 6:05 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow

Re: [Freesurfer] whole hemisphere is yellow

this is the contrast file with the corrected and uncorrected map right? miracle From: Douglas N Greve Sent: March 25, 2016 6:11 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow not sure what is

Re: [Freesurfer] whole hemisphere is yellow

also, i do require a username and password in order to send you the folder. From: Douglas N Greve Sent: March 25, 2016 6:11 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow not sure what is

Re: [Freesurfer] whole hemisphere is yellow

Hello Douglas, I have sent the files to you. Thank you. Best, Miracle From: Douglas N Greve Sent: March 25, 2016 6:11 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow not sure what is

Re: [Freesurfer] whole hemisphere is yellow

Hello Douglas, I just sent you the current file. Thank you. Best, Miracle From: Douglas N Greve Sent: March 25, 2016 9:35 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow I meant the glmfit

[Freesurfer] whole brain is yellow

Hello Douglas, this was the command i used "Freeview -f $ SUBJECTS_DIR / fsaverage / surf / lh.inflated -viewport 3d Once I opened freesurfer, I viewed lh.secondsessionscore1.glmdir--> cache.the30.pos.sig.cluster.mgh using the overlay icon ; and lh.secondsessioncore1.glmdir ---> cache.the30.po

Re: [Freesurfer] whole brain is yellow

rvard.edu Subject: Re: [Freesurfer] whole brain is yellow please also include all previous correspondence. We get a lot of emails here and we can't keep track of each person's case, so we have to look at the previous email chain. thanks! doug On 03/28/2016 02:00 PM, Miracle Ozzoude wrote:

Re: [Freesurfer] whole brain is yellow

Try changing the threshold. I think the threshold is set to 0 by default so you are seeing all the 0-valued voxels and it looks like the whole brain is active On 03/28/2016 02:14 PM, Miracle Ozzoude wrote: > This were the conversations leading up to it > "Hello Bruce and Douglas, > T

Re: [Freesurfer] White matter probability map.

hello doug, Thank you. 1) where can i find this lta file? I looked for it in the mri and surface folders but it wasn't there. do i need to run another command in order to generate it? 2) Is this the right command? mri_compute_volume_fractions --o pvf --reg filename.lta (location of .lta) 3)Also, Is

Re: [Freesurfer] Fw: White matter probability map. ( REPOST)

wrote: > > > > > > Sent from my BlackBerry 10 smartphone. > > *From: *miracle ozzoude > > *Sent: *Thursday, January 26, 2017 7:36 PM > > *To: *Freesurfer support list > > *Subject: *Re: [Freesurfer] White matter probability map. > > > > > >

Re: [Freesurfer] Fw: White matter probability map. ( REPOST)

On Fri, Jan 27, 2017 at 12:05 PM, Douglas N Greve wrote: > You would only use that if you wanted the pvf in the FS-specific > "talairach" space. Is that what you want? > > > On 01/27/2017 12:01 PM, miracle ozzoude wrote: > > Thanks doug for the response. can i use

Re: [Freesurfer] T2 and control points

Thanks Antonin and Bruce. Also, I wrote a recon-all script and when I tried to run it, it gave me an error (command not found). Please can anyone help me diagnosis what's wrong with my scripts. I did set my subject directory to the current folder (setenv SUBJECTS_DIR /../folder/; cd /.

Re: [Freesurfer] T2 and control points

Thank you very much Antonin. It worked. Best, Paul On Tue, Feb 7, 2017 at 2:36 PM, Antonin Skoch wrote: > Dear Paul, > > I don't know it it solves your problem, but if you are using bash shell, you > have to source SetUpFreeSurfer.sh, not SetUpFreeSurfer.csh. > > And, do you have FREESURFER_HOM

Re: [Freesurfer] Expert file for recon-all -hires

Hello Falk Chris and Antonin, The default is 55 https://surfer.nmr.mgh.harvard.edu/fswiki/mris_inflate. Best, Paul On Thu, Feb 9, 2017 at 10:42 AM, Falk Lüsebrink wrote: > Dear Chris and Antonin, > > I found in some archived message or in the wiki that the default used to > be 50 iterations at s

Re: [Freesurfer] Expert file for recon-all -hires

hello antonin, Thanks for the correction. Best, Paul On Thu, Feb 9, 2017 at 12:21 PM, Antonin Skoch wrote: > Dear Paul, > > for the most recent version 6.0 the default is 10. > > Looking at the help of mris_inflate binary and also to the source code. > > Antonin > > > Hello Falk Chris and Antoni

[Freesurfer] surface based PET analysis.

Hello Freesurfer, I want to perform surface based PET analysis but I can't seem to find a link for it. Please can someone direct it to me. Thanks. Best, Paul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailm

Re: [Freesurfer] Fw: PETsurfer mri_coreg problem

Hello Antonin and Doug, I viewed it in tkregister2 and I think the co-registration worked. Is there a way to extract info from both PET and anatomical to confirm the co-registration? Best, Paul On Sun, Feb 26, 2017 at 4:49 PM, Antonin Skoch wrote: > Dear Paul, > > I think that the transform win

Re: [Freesurfer] Fw: PETsurfer mri_coreg problem

gt; need to extract? > > On 2/27/17 9:03 AM, miracle ozzoude wrote: > > Hello Antonin and Doug, > > I viewed it in tkregister2 and I think the co-registration worked. Is > there a way to extract info from both PET and anatomical to confirm the > co-registration? > Best, >

Re: [Freesurfer] Fw: PETsurfer mri_coreg problem

the > coordinates tell you? > > On 2/27/17 11:01 AM, miracle ozzoude wrote: > > Hello Doug, > Thanks for replying. I meant like coordinate points on both images to > compare (i.e., any metric different from visual inspection). > Best, > Paul. > > On Mon, Feb 27, 2017

[Freesurfer] multiple expert options files/ wm and control points

Hello Freesurfer, I have couple questions. 1) If I have 2 commands (e.g., mri_normalize -a 30 and mris_inflate -n 30) and I want recon-all to execute both commands. Should I create 2 different expert opts files or 1 expert opts file with both commands in it? Also, how do I include the expert flag w

Re: [Freesurfer] multiple expert options files/ wm and control points

Thanks Antonin. For 3) what does " min #of neighbors which must be on to retain a point/specify fill_holes threshold" mean exactly? Also, I noticed a difference in FS v5.3 and FS v6.0 ReconAllTable for creating white matter surface. For v5.3, ?h.white is created as one of the outputs for mris_make_

Re: [Freesurfer] recon-all exited with error.

Thanks Antonin. Also, I got this error.log file in my label folder. Do you think it is due to the slash problem? Best, Paul On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch wrote: > Dear Paul, > > I suppose the clue is following messages from your recon-all.log file: > > FREESURFER_HOME /opt/freesu

Re: [Freesurfer] recon-all exited with error.

Hey Antonin, Thank you. hence, the right path should be "setenv FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer " Best, Paul. On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch wrote: > Dear Paul, > > the slash problem prevents to properly create symbolic link to fsaverage in > your SUBJECTS_DIR.

Re: [Freesurfer] recon-all exited with error.

Thanks. Z K Best, Paul On Fri, Mar 3, 2017 at 12:14 PM, Z K wrote: > Im looking into this now, but I think their might be a bug when using > the -parallel flag on Mac platforms. I should have a fix shortly. I will > let you know. > > On 03/03/2017 12:10 PM, miracle ozzoude wr

Re: [Freesurfer] recon-all exited with error.

Hello Z K, Were you able to fix the bug? Best, Paul On Fri, Mar 3, 2017 at 12:14 PM, Z K wrote: > Im looking into this now, but I think their might be a bug when using > the -parallel flag on Mac platforms. I should have a fix shortly. I will > let you know. > > On 03/03/2017 12

Re: [Freesurfer] recon-all exited with error.

ould > you please > source freesurfer, then run the following command. > > $> sudo -E fs_update > > (This will update a freesurfer file on your machine). Then retry the > subject with the parallel flag. Please let me know how it goes. Thanks. > > -Zeke > > On Mar 6

[Freesurfer] PETsurfer surface based analysis

Hello, I am working through the PETsurfer surface based analysis and i have couple of question a) Since the procedure is the same as surface based analysis for cortical thickness except mri_vol2surf, Can I use the procedure for thickness? b) What is the difference between mris_preproc and mri_conca

Re: [Freesurfer] Fw: PETsurfer surface based analysis

rform multimodal analysis? This is because contrast matrices are based on regressors and class in fsgd files. Best, Paul On Wed, Mar 22, 2017 at 1:11 PM, Douglas Greve wrote: > > > On 3/22/17 11:02 AM, miracoo...@gmail.com wrote: > > > > Sent from my BlackBerry 10 smartphone.

Re: [Freesurfer] Fw: PETsurfer surface based analysis

ed, Mar 22, 2017 at 3:07 PM, Douglas Greve wrote: > > > On 3/22/17 2:02 PM, miracle ozzoude wrote: > > Hello Doug, > Thank you for the detailed reply. I do have other questions. > > 1) Can you confirm if this is the correct use of mris_preproc for Uncached > PET data. m

Re: [Freesurfer] Fw: PETsurfer surface based analysis

Never mind Doug. I was able to solve the problem. Best, Paul On Wed, Mar 22, 2017 at 3:34 PM, miracle ozzoude wrote: > Thank you Doug. I am trying to perform pvc for my pet data based on the > tutorial however, I keep getting this error: > > &quo

[Freesurfer] PETsurfer output error

Hello Freesurfer, I am trying to concat my surface pet file using mris_preproc but I get this error with no output folder or files " mris_preproc --fsgd Pet.fsgd --target fsaverage --hemi lh --is C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --is C6_01_003_140908/lh.mgx.ctxgm.C

Re: [Freesurfer] PETsurfer output error

saverage.sm00.nii.gz --o > all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz > > > > On 04/07/2017 12:14 PM, miracle ozzoude wrote: > > Hello Freesurfer, > > I am trying to concat my surface pet file using mris_preproc but I > > get this error with no output folder or files " mris_preproc --fsgd >

Re: [Freesurfer] PETsurfer output error

mask to lh.pet.glmdir/mask.mgh Reshaping mriglm->mask... search space = 33150.306332 DOF = -2 ERROR: DOF = -2 Thanks, Paul On Fri, Apr 7, 2017 at 12:33 PM, Douglas N Greve wrote: > mri_concat does not take the fsgd file > > > On 04/07/2017 12:25 PM, miracle ozzoude wrote: &g

[Freesurfer] mri_glmfit error with aparc table flag

Hello freesurfer, I am trying to run mri_glmfit with the --table flag. My aparc_lh_thick_stats.txt contain entorhinal and parahippocampal thickness values for 32 subjects. I ran the glm command and received an error. Please, how can i solve this issue? I have included my command, fsgd file, contras

Re: [Freesurfer] mri_glmfit error with aparc table flag

r with aparc table flag > > Don't include --surf fsaverage lh. It thinks the input is a surface, not a > table > > > > On 4/18/17 9:21 PM, miracle ozzoude wrote: > > Hello freesurfer, > I am trying to run mri_glmfit with the --table flag. My > aparc_lh_thick_stats

Re: [Freesurfer] mri_glmfit error with aparc table flag

erry 10 smartphone. > *From: *Douglas Greve > *Sent: *Tuesday, April 18, 2017 9:52 PM > *To: *freesurfer@nmr.mgh.harvard.edu > *Reply To: *Freesurfer support list > *Subject: *Re: [Freesurfer] mri_glmfit error with aparc table flag > > Don't include --surf fsaverage lh. It t

Re: [Freesurfer] Fwd: fix topology problem

Hello Doug, No, the cerebellum has been removed. Best, Paul On Wed, Apr 19, 2017 at 1:13 PM, Douglas N Greve wrote: > Did you check to see whether cerebellum as still attached in the wm.mgz > file? > > > On 04/18/2017 09:06 PM, miracle ozzoude wrote: > > > > -

Re: [Freesurfer] mri_glmfit error with aparc table flag

as N Greve wrote: > It is a table of data, so you can't visualize it directly on anything. > You can try using annotval2surfoverlay.m to create a surface overlay of > the data. > > > On 04/19/2017 10:05 AM, miracle ozzoude wrote: > > Hello Doug, > > It worked. T

Re: [Freesurfer] Fwd: fix topology problem

see whether cerebellum as still attached in the > > wm.mgz > > file? > > > > > > On 04/18/2017 09:06 PM, miracle ozzoude wrote: > > > > > > -- Forwarded message -- > > > From: *miracle ozzoude* mirac

Re: [Freesurfer] mri_glmfit error with aparc table flag

/19/2017 01:42 PM, miracle ozzoude wrote: > > Thanks Doug. However, I am running freesurfer analysis on my personal > > computer and I don't have matlab. Also, I don't know how this matlab > > script works/ matlab works. Any instructions on how to use it or > >

Re: [Freesurfer] mri_glmfit error with aparc table flag

CTAVE_LIB /Applications/octave/lib setenv FS_OCTAVE_BIN /Application/octave/binary On Wed, Apr 19, 2017 at 3:39 PM, Douglas N Greve wrote: > I think that will work > > > On 04/19/2017 03:33 PM, miracle ozzoude wrote: > > Hello Doug, > > Do you think writing the scri

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