Re: [Freesurfer] error loading surface on one machine, but not another

Sure, glad it worked out. I like the easy solutions :) > On Dec 13, 2013, at 10:21 PM, Ryan Mruczek wrote: > > Yes, and they indeed do not match up on the two machines. I transferred > twice, not sure why there would be this issue with just the lh files. I > changed ftp programs and that see

Re: [Freesurfer] error loading surface on one machine, but not another

Yes, and they indeed do not match up on the two machines. I transferred twice, not sure why there would be this issue with just the lh files. I changed ftp programs and that seems to work. Thanks for pointing me toward in the (now) obvious route of doing the checksums. Cheers, Ryan On Dec 1

Re: [Freesurfer] segmentation incorrectly after recon-all

Hi Bruce, I upload the sugject "lilei" to your e-mail which is the segmentation incorrectly in -surfs. Thanks for your helping check it. All the best. 2013-12-14 Rujing Zha 发件人：Bruce Fischl 发送时间：2013-12-14 05:27 主题：Re: [Freesurfer] segmentation incorrectly after recon-all 收件人："Rujing Zha"

Re: [Freesurfer] problem creating annotation using mri_sample_parc?

Thank you Bruce, I read that mris_sample_parc "samples a volumetric parcellation onto a surface". I understand that this is like creating from a file of the type of aseg a corresponding file of the type of aparc.annot.ctab. Is this not true? Do I actually have to create the aparc.annot.ctab typ

Re: [Freesurfer] problem creating annotation using mri_sample_parc?

Hi Markus you need to create that file (or update FreeSurferColorLUT.txt) to reflect whatever you have in /Documents/myROIfile.mgz cheers Bruce On Sat, 14 Dec 2013, Markus Gschwind wrote: Dear Bruce, Thank you for your answer. I have not yet gotten it correctly. 1) Where does that file com

Re: [Freesurfer] problem creating annotation using mri_sample_parc?

Dear Bruce, Thank you for your answer. I have not yet gotten it correctly. 1) Where does that file come from? Should I create it? how? 2) what is missing in the command of mris_sample_parc? Why does it now work? 3) what does the second error mean? CTABfindAnnotation: ct was NULL No such file or

Re: [Freesurfer] error loading surface on one machine, but not another

can you checksum the files on both machines? On Fri, 13 Dec 2013, Ryan Mruczek wrote: > Hi All > > I created surfaces for a particular subject on one machine, and subsequently > copied the entire subjects surface directory to another machine (both running > OSX, although different versions). O

Re: [Freesurfer] problem creating annotation using mri_sample_parc?

Hi Markus that file translates indices/annotations into colors to display and human reasable names. cheers Bruce On Fri, 13 Dec 2013, Markus Gschwind wrote: I can precise the question, actually there are three: 1) ist the command correct? mris_sample_parc -v -sdir subject001 rh

[Freesurfer] error loading surface on one machine, but not another

Hi All I created surfaces for a particular subject on one machine, and subsequently copied the entire subjects surface directory to another machine (both running OSX, although different versions). On the second machine, I cannot load the lh surfaces files. For example % tksurfer LS lh white

Re: [Freesurfer] segmentation incorrectly after recon-all

I guess you should upload the subject and we will take a look On Fri, 13 Dec 2013, Rujing Zha wrote: Hi Bruce, Here is my -aseg pitcutre in the attachment. The Sgmtn lable is Right-choroid-plexus. It is my understand that the aseg looks fine. Bruce, can you tell me how to fix the -surfs? Thank

Re: [Freesurfer] Output of recon-all -all -openmp 8 does not show brainmask.mgz

Hello Pablo, Please send me the recon-all.log file for the subject and I will take a look. -Zeke On 12/13/2013 03:41 PM, pablo najt wrote: > Dear FS, > I am checking on the outputs of recon-all -all using the flag -openmp 8. > As I did with standard recon-all -all comand line I was trying to ch

[Freesurfer] Output of recon-all -all -openmp 8 does not show brainmask.mgz

Dear FS, I am checking on the outputs of recon-all -all using the flag -openmp 8. As I did with standard recon-all -all comand line I was trying to check brainmask.mgz, but there is not such file. Is there anything wrong with my outputs? Or I should be checking a different file? Thank you, Pablo

Re: [Freesurfer] mri_convert Siemens .IMA error

Hi Paul, I was finally able to track down the bug. You can get a new version from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mri_convert.macos copy it to $FREESURFER_HOME/bin/mri_convert doug On 12/08/2013 06:28 PM, prasser wrote: > Hi Doug, > > Sorry for the dela

[Freesurfer] upgrading to freesurfer 5.3

Hi Anastasia, I was hoping to upgrade to Freesurfer 5.3 in order to use the new motion detection feature of Tracula. The issue is that all of the preprocessing has already been completed in Freesurfer 5.2 with the older version of Tracula. Would I need to redo all the preprocessing in 5.3 in ord

Re: [Freesurfer] LME model

Thanks a lot Jorge, that's a big help. On 12 December 2013 23:54, jorge luis wrote: > Hi Sean > > An important issue in the LME model concerns the centering of the times > of measurement. It changes the interpretation of both the mean response and > the variance of the random effects. If tij

Re: [Freesurfer] qdec analysis with 2 covariates

I would have thought that it would have gotten all of them. You can try something like --cwp .9 On 12/13/2013 01:03 PM, Jon Wieser wrote: > HI doug > thanks, that worked. it captured from 3-13 clusters for each contrast, > not quite the 30-45 that I was seeing in the GUI. > perh

Re: [Freesurfer] funcroi commands

Yes, the edges might not be right on because it is being sampled into a 2mm space. If you play with the --fillthresh you might be able to make it line up better. On 12/13/2013 12:55 PM, Emily Boeke wrote: > Ok, it doesn't seem shifted anymore, but it is still not exactly the same as > the lab

Re: [Freesurfer] funcroi commands

Ok, it doesn't seem shifted anymore, but it is still not exactly the same as the label. Is this to be expected? Emily On Dec 13, 2013, at 11:46 AM, Douglas N Greve wrote: > > sorry, the command I gave you is not quite right. Use > > --regheader $SUBJECTS_DIR/fsaverage/mri/orig.mgz > > instea

Re: [Freesurfer] qdec analysis with 2 covariates

use the command I gave you before just add --cwp .99 to it doug On 12/13/2013 12:25 PM, Jon Wieser wrote: > Hi doug > it's requesting the --sim option > > mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 > ERROR: must spec --sim > > > > mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --si

Re: [Freesurfer] .nii file visualization in tkmedit

Thanks Doug, now it is working perfectly! On Fri, Dec 13, 2013 at 6:05 PM, Douglas N Greve wrote: > > Run > tkregister2 --mov MEG_ROI.nii --targ path/to/spm8/canonical/single_subj_T1.nii > --regheader --reg reg1.dat > mri_matrix_multiply -im reg1.dat -im Mikel_SingleSubject_to_Colin.dat -om > fi

Re: [Freesurfer] qdec analysis with 2 covariates

Hi doug it's requesting the --sim option mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 ERROR: must spec --sim mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --sim ERROR: flag --sim requires four arguments what args do I give the --sim! Jon - Original Message - From: "Doug

Re: [Freesurfer] qdec analysis with 2 covariates

sorry, it is --cwp On 12/13/2013 12:12 PM, Jon Wieser wrote: > HI Doug > MRI_glmfit-sim didn't recognize the --cwd option > > > mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99 > ERROR: Flag --cwd unrecognized. > --glmdir MTA_ADHD_MJ --cwd .99 > > > > > > > - Original Message - > From: "Do

Re: [Freesurfer] qdec analysis with 2 covariates

HI Doug MRI_glmfit-sim didn't recognize the --cwd option mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99 ERROR: Flag --cwd unrecognized. --glmdir MTA_ADHD_MJ --cwd .99 - Original Message - From: "Douglas N Greve" To: "Jon Wieser" Cc: "freesurfer" Sent: Friday, December 13, 2013 1

Re: [Freesurfer] .nii file visualization in tkmedit

Run tkregister2 --mov MEG_ROI.nii --targ path/to/spm8/canonical/single_subj_T1.nii --regheader --reg reg1.dat mri_matrix_multiply -im reg1.dat -im Mikel_SingleSubject_to_Colin.dat -om final.reg.dat Then use final.reg.dat doug On 12/13/2013 11:56 AM, Garikoitz Lerma-Usabiaga wrote: > Hi Doug,

Re: [Freesurfer] .nii file visualization in tkmedit

Hi Doug, this is what I did. This system worked in other occasions. Could it be the problem how the volume MEG_ROI.nii was created? My colleague had a Matlab matrix of 256x256x256 and he converted it to a .nii file. The registration matrix between single_subj_T1.nii and Colin27 is the following on

Re: [Freesurfer] .nii file visualization in tkmedit

Hi Doug, this is what I did. This system worked in other occasions. Could it be the problem how the volume MEG_ROI.nii was created? My colleague had a Matlab matrix of 256x256x256 and he converted it to a .nii file. The registration matrix between single_subj_T1.nii and Colin27 is the following on

Re: [Freesurfer] qdec analysis with 2 covariates

I'm sure that those clusters are not very significant. Try running mri_glmfit-sim with --cwd .99 to capture all clusters doug On 12/12/2013 03:27 PM, Jon Wieser wrote: > HI Doug, > here's a screen shot, showing the clusters and a scatter plot for one of the > 45 clusters. > for this dataset, u

Re: [Freesurfer] .nii file visualization in tkmedit

Try registering path/to/spm8/canonical/single_subj_T1.nii to Colin with bbregister doug On 12/13/2013 11:09 AM, Garikoitz Lerma-Usabiaga wrote: > Hi list, > I am trying to visualize a .nii ROI coming from MEG, which is in > Colin27 space. > > I can visualize it perfectly in mricron and tkmedit

Re: [Freesurfer] funcroi commands

sorry, the command I gave you is not quite right. Use --regheader $SUBJECTS_DIR/fsaverage/mri/orig.mgz instead doug On 12/13/2013 09:17 AM, Emily Boeke wrote: > Hi Doug, > > I tried the mri_label2vol command but the mask created does not match the > label. The mask is shifted so that it's post

[Freesurfer] .nii file visualization in tkmedit

Hi list, I am trying to visualize a .nii ROI coming from MEG, which is in Colin27 space. I can visualize it perfectly in mricron and tkmedit with the following command: tkmedit -f path/to/spm8/canonical/single_subj_T1.nii -overlay MEG_ROI.nii -fthresh 0.5 (single_subj_T1.nii is Colin27) but when

Re: [Freesurfer] funcroi commands

Hi Doug, I tried the mri_label2vol command but the mask created does not match the label. The mask is shifted so that it's posterior to the label (by ~15 slices), and the shape of the blob is a little different. Any idea why this may be? Emily On Dec 12, 2013, at 2:11 PM, Douglas N Greve wrote

Re: [Freesurfer] segmentation incorrectly after recon-all

Is that ventricle? Check the aseg and correct it if needed Cheers Bruce > On Dec 13, 2013, at 3:12 AM, "Rujing Zha" wrote: > > Dear all, > How can I fix the false segmentation in the attachment. > Thanks. > All the best. > > 2013-12-13 > Rujing Zha > > _

Re: [Freesurfer] problem creating annotation using mri_sample_parc?

I can precise the question, actually there are three: 1) ist the command correct? mris_sample_parc -v -sdir subject001 rh ~/Documents/myROIfile.mgz > rh.myROIfile.annot > 2) I do not understand the meaning of this claimed file cma_parcellation_colors.txt Actually this does not exist. In the Wik