Re: [Freesurfer] mri_glmfit-sim error

.mgh.harvard.edu on behalf of mariangela asimina *Sent:* Monday, March 20, 2023 8:13 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] mri_glmfit-sim error External Email - Use Caution Hello FreeSurfer developers and experts, I am trying to do cluster correction with mri_

Re: [Freesurfer] mri_glmfit-sim error

: Monday, March 20, 2023 8:13 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_glmfit-sim error External Email - Use Caution Hello FreeSurfer developers and experts, I am trying to do cluster correction with mri_glmfit-sim after running mri_glmfit. The command I ran

[Freesurfer] mri_glmfit-sim error

External Email - Use Caution Hello FreeSurfer developers and experts, I am trying to do cluster correction with mri_glmfit-sim after running mri_glmfit. The command I ran:   mri_glmfit-sim --glmdir lh.volume.SCNStudyTest.10.glmdir --cache 3.0 abs --cwp 0.05 --2spaces

Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

f Tarumi Takashi > > Sent: Thursday, January 20, 2022 7:59 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized > > External Email - Use Caution > > Dear Dr. Yendiki, > > Thank you so much f

Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tarumi Takashi Sent: Thursday, January 20, 2022 7:59 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized External Email - Use Caution Dear Dr

Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

tak...@gmail.com> > *Sent:* Wednesday, January 12, 2022 7:04 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized > > > External Email - Use Caution > > Dear FreeSurfer Developers: > > I am attempt

Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

22 7:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized External Email - Use Caution Dear FreeSurfer Developers: I am attempting to perform cluster-wise correction for the along-tract measures, as described on the Tract statistic

[Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

External Email - Use Caution Dear FreeSurfer Developers: I am attempting to perform cluster-wise correction for the along-tract measures, as described on the Tract statistics tutorial (

Re: [Freesurfer] mri_glmfit-sim error

This happens because the cached p-values were generated from a simulation that only went up to 30mm FWHM of smoothing. lGI has lots of internal smoothness which often pushes it over this level. You can try not using any smoothing, or, even better, try using permutation instead.

Re: [Freesurfer] mri_glmfit-sim error with no csd files generated

/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm36/pos/th40/mc-z.csd Regards, Xiaoxu From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Wednesday, January 13, 2021 9:16 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit

Re: [Freesurfer] mri_glmfit-sim error with no csd files generated

When you use --cache, mri_glmfit-sim will use precomputed (ie, "cached") CSD files as found in $FREESURFER_HOME/average/mult-comp-cor On 1/5/2021 4:55 PM, Na, Xiaoxu wrote: External Email - Use Caution Dear Freesurfer Experts, I’ve all the subjects successfully done recon-all, lgi

[Freesurfer] mri_glmfit-sim error with no csd files generated

External Email - Use Caution Dear Freesurfer Experts, I've all the subjects successfully done recon-all, lgi before coming to the group analysis. The following group analysis will use the 10mm smoothing as generated in previous recon-all. Mris_preproc were implemented

Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

External Email - Use Caution Hi Doug, Deleting the .csd files and re-running worked. Thank you! Meaghan On Tue, Sep 15, 2020 at 11:30 AM Douglas N. Greve wrote: > *Message sent from a system outside of UConn.* > > Hmm, there should have been a lot more terminal output than

Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

Hmm, there should have been a lot more terminal output than that. Try this, delete the CSD files: rm lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j*-osgm.csd Then re-run. If it fails, then send me the perm.th20.abs.j*-osgm.csd files On 9/14/2020 2:58 PM, Meaghan Perdue wrote:

Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

External Email - Use Caution Hi Doug, Here is the command: mri_glmfit-sim --glmdir lh.rs6980093.thickness10.glmdir --perm 1000 2.0 abs --cwp 0.05 --2spaces --bg 4 And here is the output: mri_glmfit simulation done 4.78645 mri_glmfit simulation done 4.806 mri_glmfit

Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

please send the full command line and terminal output On 9/9/2020 3:19 PM, Meaghan Perdue wrote: External Email - Use Caution Hello Freesurfer experts, We're receiving the following error message when trying to run mri_glmfit-sim: ERROR: CSDmerge: CSDs have same seed This only

[Freesurfer] mri_glmfit-sim error CSDs have the same seed

External Email - Use Caution Hello Freesurfer experts, We're receiving the following error message when trying to run mri_glmfit-sim: ERROR: CSDmerge: CSDs have same seed This only occurs when we try to run the permutation on the LH for thickness. We've been able to run the

Re: [Freesurfer] mri_glmfit-sim error

See this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm On 2/7/2020 9:52 PM, Kim, Gwang-Won wrote: Hi there, I ran “mri_glmfit-sim –glmdir g2v3.wls –2spaces –perm 1000 1.3 abs”. But, there was error message as follow: “design matrix is not orthogonal,

[Freesurfer] mri_glmfit-sim error

Hi there, I ran “mri_glmfit-sim -glmdir g2v3.wls -2spaces -perm 1000 1.3 abs”. But, there was error message as follow: “design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with -perm-force” Please let me know how to process

Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

External Email - Use Caution Hi Freesurfer, I am also experiencing the same problem and everything regarding FREESURFER path looks ok just getting error that says: Reading source surface /storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white MRISread(): could not open

Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

On 11/27/2018 06:46 AM, C.P.E. Rollins wrote: > External Email - Use Caution > Hi Douglas, > > Thanks a lot for your answers. > > 1) For the permutations, would you recommend using this for > controlling for MC in cortical thickness analyses too? Yes > Why is it recommended to use permutation

Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

External Email - Use Caution Hi Douglas, Thanks a lot for your answers. 1) For the permutations, would you recommend using this for controlling for MC in cortical thickness analyses too? Why is it recommended to use permutation simulation as opposed to Z Monte Carlo simulation

Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

On 11/23/2018 11:26 AM, C.P.E. Rollins wrote: > External Email - Use Caution > Dear Freesurfer Developers, > I have a 2-part question: > 1) I was advised to use permutation to control for multiple > comparisons in an LGI analysis, would you mind elaborating how to do > this in command line

[Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

External Email - Use Caution Dear Freesurfer Developers, I have a 2-part question: 1) I was advised to use permutation to control for multiple comparisons in an LGI analysis, would you mind elaborating how to do this in command line (in terms of command and parameters)? 2) In

[Freesurfer] mri_glmfit-sim error

External Email - Use Caution Dear Freesurfer Developers, I'm trying to run mri_glmfit-sim to correct for multiple comparisons but am receiving the following error: cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir

Re: [Freesurfer] mri_glmfit-sim error

External Email - Use Caution Hi Douglas, Yes, the file (/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white) exists, I can view it in Freeview and have read permissions. I had recently tried downloading this patch:

Re: [Freesurfer] mri_glmfit-sim error

Can you verify that the followign file exists, that you have read permission, and that you can successfully load it into freeview? /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white On 9/21/18 11:41 AM, C.P.E. Rollins wrote: External Email - Use Caution Hello

[Freesurfer] mri_glmfit-sim error

External Email - Use Caution Hello Freesurfer Developpers, I'm trying to use mri_glmfit-sim to make clusterwise corrections but am running into the following error: - XFM matrix (RAS2RAS) ---

Re: [Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file

Is this for a volume analysis? If so, then you'll need to use the --grf option instead of using the mcz simulations (those are just for surface) On 07/08/2017 01:03 PM, Aly Negreira wrote: > Hi Doug! > > Thank you for the reply! Re-ran w/ --debug as first option. Below is > the output. Not

Re: [Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file

Hi Doug! Thank you for the reply! Re-ran w/ --debug as first option. Below is the output. Not sure if this is helpful, but when I cd to /Applications/freesurfer/average/mult-comp-cor/fsaverage there are only directories for lh and rh, nothing for mni. Thanks for the help! Aly

Re: [Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file

Hi Aly, it is not creating the path correctly, not sure why. Can you run it again with --debug as the first option and send me the terminal output? doug On 7/1/17 1:57 PM, Aly Negreira wrote: Hi Freesurfer Community, I'm using FsFast on my dissertation data and trying to run a monte carlo

[Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file

Hi Freesurfer Community, I'm using FsFast on my dissertation data and trying to run a monte carlo correction on my functional data in the volume. I keep running into the below error. In attempting to troubleshoot, it looks like Yuko ran into a similiar issue (see archived email from Fri Dec 9 @

Re: [Freesurfer] mri_glmfit-sim error

rojectoutputdata/rh.paired-diff.glmdir/y.fsgd dods >> --surf fsaverage rh white >> simbase >> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001 >> FWHM = -nan >> ERROR: input FWHM is NaN (not a number). >> Check the mask

Re: [Freesurfer] mri_glmfit-sim error

...@nmr.mgh.harvard.edu] Sent: Monday, May 09, 2016 5:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim error It looks like over half your voxels have been pruned because they have value identical to 0 in at least one subject Found 149926 points in label. Pruning voxels by thr

Re: [Freesurfer] mri_glmfit-sim error

>Check the mask in the glm directory. > Mon May 9 09:11:28 CDT 2016 > ERROR: cannot find any csd files > > ------------- > > Many thanks for helping me with this Doug. > > Regards &

Re: [Freesurfer] mri_glmfit-sim error

oun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, May 06, 2016 3:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim error something is going wrong because the FWHM is not-a-number (

Re: [Freesurfer] mri_glmfit-sim error

44094.721767 > > Thanks > Koushik > > ___ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, May 06, 2016 10:46 AM >

Re: [Freesurfer] mri_glmfit-sim error

___ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, May 06, 2016 10:46 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim error The problem

Re: [Freesurfer] mri_glmfit-sim error

The problem is with the estimate of the FWHM for that run. Can you re-run mri_glmfit and send me the command line and terminal output? On 05/06/2016 10:27 AM, Govindarajan, Koushik Athreya wrote: > Dear FS experts, > > I ran into an error with one of my mri_glmfit-sim execution > and

[Freesurfer] mri_glmfit-sim error

Dear FS experts, I ran into an error with one of my mri_glmfit-sim execution and was not sure what was going on. The same simulation is currently running for the left hemisphere without any hiccups but I get this following error for the right hemisphere:

Re: [Freesurfer] mri_glmfit-sim error

Use "abs" not "" On 09/04/2015 03:20 PM, Xiaomin Yue wrote: > Hi, > > I got this error when run mri_glmfit-sim: missing name for redirect. > I am running freesurfer 5.3. the command is: mri_glmfit --glmdir > ces.nii --cache 2 --sim-sign . The ces.nii was generated from > group level

Re: [Freesurfer] mri_glmfit-sim error

Thanks Xiaomin On Tue, Sep 8, 2015 at 2:03 PM -0700, "Douglas N Greve" wrote: Use "abs" not "" On 09/04/2015 03:20 PM, Xiaomin Yue wrote: > Hi, > > I got this error when run mri_glmfit-sim: missing name for redirect. > I am running freesurfer 5.3. the command

[Freesurfer] mri_glmfit-sim error

Hi, I got this error when run mri_glmfit-sim: missing name for redirect. I am running freesurfer 5.3. the command is: mri_glmfit --glmdir ces.nii --cache 2 --sim-sign . The ces.nii was generated from group level analysis (isxconcat-sess). Thanks for your help. Xiaomin

[Freesurfer] mri_glmfit-sim Error

Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows:  mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166

Re: [Freesurfer] mri_glmfit-sim error

: [Freesurfer] mri_glmfit-sim error what is the error? I did not see anything in the log file. On 10/24/2014 04:18 AM, wrz891...@163.com wrote: Dear Freesurfer Experts, I'm a new freesurfer, it comes some errors whendoing mri_glmfit-sim analysis. I don't konw what is wrong about

[Freesurfer] mri_glmfit-sim error

Dear Freesurfer Experts, I'm a new freesurfer , it comes some errors when doing mri_glmfit-sim analysis. I don't konw what is wrong about it ,it just never work when doning at mri_glmfit-sim ,and my commands as follwing. mris_preproc --fsgd advsnc.fsgd \ --cache-in

Re: [Freesurfer] mri_glmfit-sim error

what is the error? I did not see anything in the log file. On 10/24/2014 04:18 AM, wrz891...@163.com wrote: Dear Freesurfer Experts, I'm a new freesurfer, it comes some errors whendoing mri_glmfit-sim analysis. I don't konw what is wrong about it ,it just never work when # doning at

Re: [Freesurfer] mri_glmfit-sim error

Thanks a lot ! It just stopped woking at the last line and it didn't generate the results ,so I didn't konw how to deal whit it . wrz891...@163.com From: Douglas N Greve Date: 2014-10-25 00:32 To: freesurfer Subject: Re: [Freesurfer] mri_glmfit-sim error what is the error? I did

[Freesurfer] MRI_glmfit-sim error

I'm running a monte carlo sim and am getting an error: command line: mri_glmfit-sim \ --glmdir MTA_persistanceCP \ --sim mc-z 1000 1.3 mc-z.negative \ --sim-sign abs --cwpvalthresh 0.999 \ --overwrite output: cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh --fsgd

Re: [Freesurfer] MRI_glmfit-sim error

I'm not sure how that could have happened. Did you run mri_glmfit multiple times by any chance? On 07/29/2014 03:10 PM, Jon Alan Wieser wrote: I'm running a monte carlo sim and am getting an error: command line: mri_glmfit-sim \ --glmdir MTA_persistanceCP \ --sim mc-z 1000 1.3

Re: [Freesurfer] MRI_glmfit-sim error

To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MRI_glmfit-sim error I'm not sure how that could have happened. Did you run mri_glmfit multiple times by any chance? On 07/29/2014 03:10 PM, Jon Alan Wieser wrote: I'm running a monte carlo sim and am getting an error: command

Re: [Freesurfer] MRI_glmfit-sim error

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MRI_glmfit-sim error I'm not sure how that could have happened. Did you run mri_glmfit multiple times by any chance? On 07/29/2014 03:10 PM, Jon Alan Wieser wrote: I'm running a monte carlo sim and am getting an error: command line

[Freesurfer] mri_glmfit-sim error

Hello list, I'm working with FS 5.0.3. When I used 'mri_glmfit-sim --glmdir /home/a/freesurfer/g2.lh/C1 --sim mc-z 5000 4 mc-z.abs --sim-sign abs --cwpvalthresh 0.05 --overwrite' for multiple comparison correction, i got an error message 'cannot find /.../g2.lh/C1/mri_glmfit.log'. I found a

[Freesurfer] mri_glmfit-sim Error

After running a group comparison using qdec I wanted to use mc-z for multiple comparison correction I tried running: mri_glmfit-sim \ --glmdir MTA_ADHD_MJ2 \ --sim mc-z 1000 2.0 mc-z.negative \ --sim-sign abs --cwpvalthresh 0.999 \ --overwrite ERROR: dimension mismatch between X

Re: [Freesurfer] mri_glmfit-sim error

Doug -- Sorry for asking your help again as I can't seem to resolve this on my own. I looked up the mri_glmfit-sim --help and added the path of csd file in the argument, but it still fails to find .csd file. Can you let me know once again what I did wrong? (see the command line below).

Re: [Freesurfer] mri_glmfit-sim error

Hi Doug, I tried as you suggested, but i've got the following error: e.g.,cannot find any csd files. However, I can see them stored in csd folder as shown below: /2D/results/LH/GLM/csd ls mc-z.negative.j001-osgm.csd perm.abs.2.j001-osgm.csd I'm guessing that I need to define the path for this

Re: [Freesurfer] mri_glmfit-sim error

--no-sim takes an argument. Run mri_glmfit-sim with --help to get more info doug On 06/04/2013 09:11 AM, Glen Lee wrote: Hi Doug, I tried as you suggested, but i've got the following error: e.g.,cannot find any csd files. However, I can see them stored in csd folder as shown below:

[Freesurfer] mri_glmfit-sim error

Hello Freesurfer experts-- I ran mri_glmfit-sim to validate the group level GLM result (which was already done using mri_glmfit), but I was not able to get any result out of it. Even with a quite liberal threshold (2), no vertices came out (below is what I typed in for the random permutation).

Re: [Freesurfer] mri_glmfit-sim error

Indeed, I initially tried 10,000 iterations and got nothing. What else then could have gone wrong? FYI, I use v5.1.0. On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: You will need more like 1 iterations instead of 100. doug On 06/03/2013 04:49 PM, Glen

Re: [Freesurfer] mri_glmfit-sim error

hi Glen, no cluster will show up if the p-value for all clusters is above .05. You can change this with --cwpvalthresh to something like .99. That should give you all the clusters. Also, you don't have to run the full simulation again; you can use the --no-sim option and it will use the

[Freesurfer] mri_glmfit-sim - error of fwhm

Dear experts, I have a error message when I use the command : mdi_glmfit-sim ‹glmdir X ‹cwpvalthresh 0,001 ‹cache 3 abs ERROR : cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage_sym/lh/cortex/fwhm00/a bs/th20/mc-z.csd I don't understand why because to create this glmdir I use a

Re: [Freesurfer] mri_glmfit-sim - error of fwhm

Hi Sophie, the problem may be that you have used 0,001 instead of 0.001. doug On 05/02/2013 10:40 AM, Sophie Maingault wrote: Dear experts, I have a error message when I use the command : mdi_glmfit-sim —glmdir X —cwpvalthresh 0,001 —cache 3 abs ERROR : cannot find

[Freesurfer] mri_glmfit-sim error

Hi all, I've got an error while running mri_glmfit-sim. I ran this for several measures, and only for 'volume' and 'area' the function complained about missing CSD files stating ERROR: cannot find any csd files I don't know if this is a known issue. I saw several threads posted regarding this

Re: [Freesurfer] mri_glmfit-sim error

Can you send your command line and terminal output? On 05/14/2012 09:26 AM, Juke Cha wrote: Hi all, I've got an error while running mri_glmfit-sim. I ran this for several measures, and only for 'volume' and 'area' the function complained about missing CSD files stating ERROR: cannot find

Re: [Freesurfer] mri_glmfit-sim error

Hi Mingxia, use --cache 1.3 neg you have it the other way around doug zhang mingxia wrote: Hi, every one, I just run the flag mri_glmfit-sim for Surface-based Correction for Multiple Comparisons as below: mri_glmfit-sim \ --glmdir lh.Chinese_fastreading_thickness.glmdir \

Re: [Freesurfer] mri_glmfit-sim error

Thank you very much!! On Wed, Jan 4, 2012 at 11:55 PM, zhang mingxia zhangmingxia1...@gmail.comwrote: Hi, every one, I just run the flag mri_glmfit-sim for Surface-based Correction for Multiple Comparisons as below: mri_glmfit-sim \ --glmdir lh.Chinese_fastreading_thickness.glmdir \

[Freesurfer] mri_glmfit-sim error

Hi, every one, I just run the flag mri_glmfit-sim for Surface-based Correction for Multiple Comparisons as below: mri_glmfit-sim \ --glmdir lh.Chinese_fastreading_thickness.glmdir \ --cache neg 1.3 \ --cwpvalthresh .025 lh.Chinese_fastreading_thickness.glmdir is the pre-cached simulation

Re: [Freesurfer] mri_glmfit-sim error

Hi Joost, the precomputed tables only go up to 30mm FWHM. The 25 mm you apply adds to some that is already there to cause it to be 31mm, so the table does not exist. I would say that 25mm is a lot to smooth by. Do you really need that much? doug j janssen wrote: Hi, - FS version: 5.1 -

Re: [Freesurfer] mri_glmfit-sim error with v5.0

Can you tar up your glmdir and drop it to me? doug Yuko Yotsumoto wrote: Thank you Doug, Hi Yuko, I think you must have an older version of glmfit-sim some how. I've put a newer version here: I replaced the /bin/mri_glmfit-sim, but got the same error. [ERROR 1] In line 292: set

Re: [Freesurfer] mri_glmfit-sim error with v5.0

Thank you Doug, Hi Yuko, I think you must have an older version of glmfit-sim some how. I've put a newer version here: I replaced the /bin/mri_glmfit-sim, but got the same error. [ERROR 1] In line 292: set csdCache =

Re: [Freesurfer] mri_glmfit-sim error with v5.0

Hi Yuko, I think you must have an older version of glmfit-sim some how. I've put a newer version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim-v5.0 copy this to your $FREESURFER_HOME/bin/mri_glmfit-sim (ie, change the name; and make a backup copy). doug

[Freesurfer] mri_glmfit-sim error with v5.0

Hello I'm having a trouble with mri_glmfit-sim with v5.0, which is locally installed on Mac 10.6.8. Whan I ran: mri_glmfit-sim --glmdir MPglm.wls --cache 3.0 pos --cwpvalthresh .0166 I got: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd I

[Freesurfer] mri_glmfit-sim error

hi folks, when i run mri_glmfit-sim --glmdir rh.measure_t7cort.glmdir --cache 2.0 neg i get an error message ERROR: cannot find /apps/x86_64_sci5/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/neg/th20/mc-z.csd there is fsaverage... should i just make a soft link ? also when

Re: [Freesurfer] mri_glmfit-sim error

You can make a soft link. Don't worry about that warning (it's not important, and I've fixed it for the next version). doug GREGORY R KIRK wrote: hi folks, when i run mri_glmfit-sim --glmdir rh.measure_t7cort.glmdir --cache 2.0 neg i get an error message ERROR: cannot find