Re: [Freesurfer] Freesurfer Start Up

Thank you, I will go there now. But regarding the output of freesurfer, the format will be .ccd? On Jul 30, 2014, at 7:23 PM, Bruce Fischl wrote: > Hi Isaiah > > you might check out MNE from Matti Hamalainen (ccd). It does all this and > more (using FreeSurfer surfaces and segmentations) >

Re: [Freesurfer] question regarding control point edits

Did it help? Try -make all Cheers Bruce > On Jul 30, 2014, at 7:50 PM, Adam Mezher wrote: > > Hi Bruce, > Thanks a lot for your help thus far. I've edited, computed, and applied the > average bias to the error subjects' orig.mgz files. However, I'm not sure how > to re-run all autorecon steps

[Freesurfer] tkmedit error

Dear experts when I use the tkedit, it report the error (in the following). How could I solve it? tkmedit started: Thu Jul 31 10:41:56 2014 /Applications/freesurfer/tktools/tkmedit.bin patient_con_sub126 brainmask.tight.mgz -aux T1.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $

Re: [Freesurfer] yet another newbie question (YANQ)

Hi Donald Yes, you can use mri_convert -rl rawavg.mgz Cheers Bruce > On Jul 30, 2014, at 8:12 PM, "Krieger, Donald N." wrote: > > Thanks for the helpful responses to the previous questions, Bruce. > It’s great to not stay stuck for long. > > Here’s another. > I am working with voxels in

Re: [Freesurfer] Freesurfer Start Up

Hi Isaiah you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces and segmentations) cheers Bruce On Thu, 31 Jul 2014, Isaiah C. Smith wrote: Thank you so much, Bruce.  I think that I got it. Overall, I am trying to create a source volume co

Re: [Freesurfer] Freesurfer Start Up

Thank you so much, Bruce. I think that I got it. Overall, I am trying to create a source volume conduction model, calculate the lead field matrix, and then create a source model. My instructor said that it might be possible to do this in Freesurfer. Sorry, I am kind of new to using the terminal

[Freesurfer] yet another newbie question (YANQ)

Thanks for the helpful responses to the previous questions, Bruce. It's great to not stay stuck for long. Here's another. I am working with voxels in the original MRI coordinate system. It appears that voxel and vertex coordinates in freesurfer are transformed to a 1 mm x 256^3 volume. Is there

Re: [Freesurfer] question regarding control point edits

Hi Bruce, Thanks a lot for your help thus far. I've edited, computed, and applied the average bias to the error subjects' orig.mgz files. However, I'm not sure how to re-run all autorecon steps for these cases using the newly created orig.mgz (with bias applied). Thoughts? Thanks, Adam H

Re: [Freesurfer] mri_binzrize (flag --wm )

Thank you Doug, Do you mean an error in the script that running this command line ?! kindly what is the number of IDs that I can add after the flag --match ? Mohamad -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf

[Freesurfer] mni152reg

Hi Freesurfer experts, I was trying to align T1 image to MNI space by running 'mni152reg --s ', and got the following error messages: mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.5197': Permission denied ... niiWrite(): error opening file

Re: [Freesurfer] proportion of surface area of significant region

You don't want to get the surface area from the faces of fsaverage. Instead use the values in fsaverage/surf/lh.white.avg.area.mgh (this is the average of the group used to create fsaverage), or, probably better, get an average area map for your cohort doug On 07/30/2014 08:38 AM, Lars M. Rimo

Re: [Freesurfer] qdec _FDR report question (why the result of cluster stats table not match with the statistic map)

what is the contrast stats table and how did you create it? On 07/30/2014 11:35 AM, Wang, Guoying wrote: > > Dear Freesurfer experts, > > I am facing the problem to report the significant clusters which was > calculated by QDEC. I did the group comparison between healthy and > patients in cortic

Re: [Freesurfer] qdec problem

The DOSS option has been removed (DODS only). Can you give more info about the threshold problem? On 07/30/2014 04:27 AM, Emilia Johansson wrote: > Hello, > > When I use qdec I can´t change the threshold values and I don't have > the Design Matrix Type option (DODS, DOSS). > > I'm using ubuntu

Re: [Freesurfer] Preprocessing Error

Is the size of the volume (row, cols, or slices) changing between the runs? On 07/30/2014 04:18 PM, bbr...@bidmc.harvard.edu wrote: > Hi Doug, > > I have been getting an error message when preprocessing data on 2 subjects in > stable 4 (using the same command worked fine, however, with several o

Re: [Freesurfer] mri_binzrize (flag --wm )

That was an error, 82 should not be in there. doug On 07/30/2014 03:07 PM, Bruce Fischl wrote: > Hi Mohamad > Right-non-WM-hypointensities are hypointense voxels (in T1 images) in > the right hemisphere in regions that are not normally white matter > (like the middle of the putamen). > > I'll l

[Freesurfer] Preprocessing Error

Hi Doug, I have been getting an error message when preprocessing data on 2 subjects in stable 4 (using the same command worked fine, however, with several others). The command I ran was: preproc-sess -smout fmcsm6 -fwhm 6 -s Con7_self -df sesspar The error message I get is pasted below. Any

Re: [Freesurfer] T2-space vs T2-space-FLAIR

thanks bruce. we aren't collecting the flair currently but some of our clinical collaborators have asked for it. we are likely to collect both on our next few participants, so happy to test out the alpha version. cheers, satra On Wed, Jul 30, 2014 at 3:08 PM, Bruce Fischl wrote: > please don'

Re: [Freesurfer] T2-space vs T2-space-FLAIR

please don't count on the T2 and FLAIR options doing the same thing as I suspect that they won't in the near future! Bruce On Wed, 30 Jul 2014, Satrajit Ghosh wrote: thanks matt, would like to be sure that your comments in relation to the T2-space-flair sequence and not the typical clinical

Re: [Freesurfer] mri_binzrize (flag --wm )

Hi Mohamad Right-non-WM-hypointensities are hypointense voxels (in T1 images) in the right hemisphere in regions that are not normally white matter (like the middle of the putamen). I'll leave your other questions for Doug cheers Bruce On Wed, 30 Jul 2014, Alshikho, Mohamad J. wrote: H

Re: [Freesurfer] T2-space vs T2-space-FLAIR

thanks matt. cheers, satra On Wed, Jul 30, 2014 at 2:58 PM, Matt Glasser wrote: > Yes we performed both on the same subject in the same session and then > compared the myelin map results. > > Peace, > > Matt. > > From: Satrajit Ghosh > Reply-To: Freesurfer support list > Date: Wednesday, Ju

Re: [Freesurfer] T2-space vs T2-space-FLAIR

Hi Satra I've been working on that this week, and I think the answer is "yes, but not a lot". The FLAIR has worked better in our past tests, but I found some problems with the T2 code and it is working much better now, so I think the jury is out. We're happy to give you an alpha version if you

Re: [Freesurfer] T2-space vs T2-space-FLAIR

Yes we performed both on the same subject in the same session and then compared the myelin map results. Peace, Matt. From: Satrajit Ghosh Reply-To: Freesurfer support list Date: Wednesday, July 30, 2014 at 1:53 PM To: Freesurfer support list Subject: Re: [Freesurfer] T2-space vs T2-space

Re: [Freesurfer] T2-space vs T2-space-FLAIR

thanks matt, would like to be sure that your comments in relation to the T2-space-flair sequence and not the typical clinical TSE-FLAIR. is that the case? cheers, satra On Wed, Jul 30, 2014 at 2:23 PM, Matt Glasser wrote: > Bruce has said the FLAIR might be a little better for FreeSurfer but

[Freesurfer] mri_binzrize (flag --wm )

Hi, I have a question about the flag " -wm" in mri_binarize: The following segments IDs 8 2 41 82 251 252 253 254 255 are included in this flag (based on the summary of this command line when I run it). Kindly what is the segment ID (Right-non-WM-hypointensities) means? and why the (left-non-WM-

Re: [Freesurfer] T2-space vs T2-space-FLAIR

Bruce has said the FLAIR might be a little better for FreeSurfer but it¹s worse for myelin maps (has less CNR for the myelin, though you can still see the major areas). Currently, the T2 and FLAIR flags do exactly the same thing, so it doesn¹t even matter what flag you use. I think it depends on

[Freesurfer] T2-space vs T2-space-FLAIR

hi bruce, is there any difference from freesurfer's perspective of using T2-space or T2-space-flair? cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

[Freesurfer] Voxel Edit Clone Broken in 5.3.0

Hi all, It looks like there’s a bug in Freeview 5.3 Voxel Edit - Clone - although the button is present, the drop down to choose a reference image is unresponsive - you can click it but it doesn’t provide a list of any of the loaded volumes - there’s no way to specify which reference to clone f

Re: [Freesurfer] Can't Recognize dicom file

Hmm... I got same error message when using the one that is right from the scanner. On Wed, Jul 30, 2014 at 12:17 PM, Bruce Fischl wrote: > Hi Yi-Yi > > is this right off the scanner? It looks like it has gone through MIPAV. > Can you try one that is right from the scanner? > cheers > Bruce > >

Re: [Freesurfer] Can't Recognize dicom file

Hi Yi-Yi is this right off the scanner? It looks like it has gone through MIPAV. Can you try one that is right from the scanner? cheers Bruce On Wed, 30 Jul 2014, Yi-Yu Chou wrote: Dear Freesurfer experts: I'm running errors when I try to run the dicom files with recon-all. It shows: ERROR:

Re: [Freesurfer] occipital lobe WM errors

Hey Bruce, I uploaded a subject that you requested a few days ago (problems with segmentation in the occipital lobe). I just wanted to make sure the file transferred successfully, and if you have had a change to analyze. Thanks, Matt On Mon, Jul 28, 2014 at 5:48 PM, Walton, Matt wrote: > Hey

[Freesurfer] Fwd: mpr2mni305 failed error

I all! I have the same problem in about 15% of MRI scans, all made with the same scanning protocol (T1 MPRAGE in a SIEMENS Avanto 1,5 T) during the recon-all -all process. I can't recognize any difference between those scans which work correctly and those not. I have never found the same error on

Re: [Freesurfer] LocalGI error {Disarmed}

OK, so there is something going wrong with your unix environment inside of matlab (this is not a freesurfer problem per se). Is there someone around that you can ask about it? Can someone else try this last command to see if it works? There might be something wrong with the resource file of th

Re: [Freesurfer] LocalGI error {Disarmed}

set: Variable name must begin with a letter. gunzip: Command not found. ans = 1 On 30 Jul 2014, at 16:27, Douglas N Greve wrote: > > And in matlab, what do you get if you type > > unix('which gunzip') > > > > > On 07/30/2014 11:08 AM, Sarina Iwabuchi wrote: >> I get: >> >> /usr/bin/

Re: [Freesurfer] LocalGI error {Disarmed}

And in matlab, what do you get if you type unix('which gunzip') On 07/30/2014 11:08 AM, Sarina Iwabuchi wrote: > I get: > > /usr/bin/gunzip > > On 30 Jul 2014, at 15:58, Douglas N Greve wrote: > >> >> Is gunzip in your path? When you open a shell and type >> which gunzip >> >> what is printed

Re: [Freesurfer] LocalGI error {Disarmed}

I get: /usr/bin/gunzip On 30 Jul 2014, at 15:58, Douglas N Greve wrote: > > Is gunzip in your path? When you open a shell and type > which gunzip > > what is printed out? > > > On 07/30/2014 10:45 AM, Sarina Iwabuchi wrote: >> Hi Bruce, >> >> It still shows the same error: >> >> set: Varia

Re: [Freesurfer] LocalGI error {Disarmed}

Is gunzip in your path? When you open a shell and type which gunzip what is printed out? On 07/30/2014 10:45 AM, Sarina Iwabuchi wrote: > Hi Bruce, > > It still shows the same error: > > set: Variable name must begin with a letter. > gunzip: Command not found. > ERROR: problem reading fname > s

Re: [Freesurfer] LocalGI error {Disarmed}

Hi Bruce, It still shows the same error: set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set: Variable name must begin with a letter. rm: Command not found. SWITCH expression must be a scalar or string constant. Error in load_mgh (line 158) sw

Re: [Freesurfer] MRI_glmfit-sim error

I deleted the output folder, then reran each contrast into a separate output folder. problem solved! Thanks! Jon From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve Sent: Tuesday, July 29, 2014 3:59 PM To: freesurfer@nmr.mgh.harvar

Re: [Freesurfer] qdec error

that fixed the problem Thanks Jon From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve Sent: Tuesday, July 29, 2014 4:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec error Try removing the mean from the a

Re: [Freesurfer] LocalGI error {Disarmed}

Hi Sarina, you need to have $FREESURFER_HOME/matlab in your matlab path. Try: addpath(sprintf('%s/matlab', getenv('FREESURFER_HOME'))) cheers Bruce On Wed, 30 Jul 2014, Sarina Iwabuchi wrote: Hi Doug, I get the following error: Undefined function 'MRIread' for input arguments of type 'cha

Re: [Freesurfer] Freesurfer Start Up

you need a "-" before each option, so it should be recon-all -help On Wed, 30 Jul 2014, Isaiah C. Smith wrote: The recon-all option is no longer working and neither is the other one. I am getting an error.  Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help

Re: [Freesurfer] Freesurfer Start Up

Hi Isaiah remove the space. It should be: recon-all cheers Bruce On Wed, 30 Jul 2014, Isaiah C. Smith wrote: The command is not found. Last login: Tue Jul 29 17:42:52 on ttys001 freesurfer-Darwin-lion-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FS

[Freesurfer] proportion of surface area of significant region

Hi Bruce, I would like to be able to tell what proportion of a region of interest (ROI), as defined in atlas space by e.g. Desikan-Killiany, that shows a significant effect (based on a p-map). For now I overlay the p-map on the inflated surface of fsaverage in tksurfer and eyeball the proportion.

[Freesurfer] NIH Staff Scientist Position available, Bethesda, MD, USA

Posted on behalf of Dr. Judy Rapoport: Department of Health and Human Services (DHHS) National Institutes of Health (NIH) National Institute of Mental Health (NIMH) Division of Intramural Research Programs (DIRP) Section on Childhood Neuropsychiatric Disorders (SCND) Child Psychiatry Branch (CPB)

Re: [Freesurfer] LocalGI error {Disarmed}

Hi Doug, I get the following error: Undefined function 'MRIread' for input arguments of type 'char'. Sarina On 29 Jul 2014, at 18:34, Douglas N Greve wrote: > a = > MRIread('/Volumes/HD-PNTU3/MISSEDDATA/extn003/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz'); Sarina Iwabuchi Division

[Freesurfer] qdec problem

Hello, When I use qdec I can´t change the threshold values and I don't have the Design Matrix Type option (DODS, DOSS). I'm using ubuntu 13.10, freesurfer 5.3.0 and qdec 1.5. Any suggestions of what can be the problem? Do I need to download something more? I don't get any error messages when I

Re: [Freesurfer] Mask custom ROI with automated parcellation (aparc)

works perfectly, thank you! On 28 July 2014 19:27, Douglas N Greve wrote: > > Does mri_mask work? > > On 07/28/2014 12:50 PM, Bastian Cheng wrote: >> Thank you, Douglas! >> >> Is there a way to mask my functional ROI with these binarized aparc ROIs? >> >> I guess what I want to do is: ROIfunctio