Re: [Freesurfer] mri_glmfit error: matrix is rank-deficient by 18

External Email - Use Caution Hi, This doesn't make a difference. I can say that the Apple M- dev version likely has an issue with the permutation procedure in runClustSims.sh. At the GLM stage, the program is still saying that the matrix is rank deficient by the number of matrix e

Re: [Freesurfer] mri_glmfit error: matrix is rank-deficient by 18

External Email - Use Caution  I’m not sure it will make a difference, but you could try downloading, installing and running one of the current development builds for the Silicon Mac.  You could try this download link, https://secure-web.cisco.com/1knximumtc7HGhko0zDsKDfS2Nqhp3y3b

[Freesurfer] mri_glmfit error: matrix is rank-deficient by 18

External Email - Use Caution *Hi FreeSurfer Developers,* *I am attempting to compute group analysis as described in the FS tutorial and it appears to run but with the following message at the end for each contrast:* Writing results CON-ACLleft maxvox sig=-2.57471 F=9.30914

Re: [Freesurfer] mri_glmfit error - matrix ill-conditioned. no solution from archive.

The scale is much different between columns 1 and 8, you may want to  normalize by subtracting the mean and dividing by the standard deviation. On 3/21/2023 1:53 PM, miracle ozzoude wrote: External Email - Use Caution Hello, Any idea how to solve this problem? I have tried the suggest

[Freesurfer] mri_glmfit error - matrix ill-conditioned. no solution from archive.

External Email - Use Caution Hello, Any idea how to solve this problem? I have tried the suggested solutions on the archive, that's Demean and Rescale but to no avail. I have attached the necessary files in the email below. Many thanks, Miracle mri_glmfit command: mri_glmfit --

Re: [Freesurfer] mri_glmfit error

Do you see where it says "ERROR: READ THIS"? And below that do you see that it asks for four things? Can you send those four things? On 10/5/2022 2:51 PM, fernanda rohrsetzer wrote: External Email - Use Caution Hi, I attempted to execute mri_glmfit on my structural data through the fo

Re: [Freesurfer] mri_glmfit error

External Email - Use Caution Ohh!! I'm so sorry for my stupidity!!! Thank you so much for your patience!!! Em seg., 3 de out. de 2022 às 10:04, Douglas N. Greve < dgr...@mgh.harvard.edu> escreveu: > those are the contrast matrices. The design matrix will be in the output > fold

Re: [Freesurfer] mri_glmfit error

those are the contrast matrices. The design matrix will be in the output folder as file Xg.txt On 9/30/2022 11:43 AM, fernanda rohrsetzer wrote: External Email - Use Caution The design matrix (examining difference in thickness after controlling for effects of age, sex and Average thi

Re: [Freesurfer] mri_glmfit error

External Email - Use Caution The design matrix (examining difference in thickness after controlling for effects of age, sex and Average thickness) 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-HR_testcov.mtx 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-MDD_testcov.mtx 0 1 -1 0 0 0 0

Re: [Freesurfer] mri_glmfit error

almost there -- you did not include the 4th ittem On 9/30/2022 11:18 AM, fernanda rohrsetzer wrote: External Email - Use Caution I'm so sorry... The FSGD file is attached (called "TestCT.txt). The design matrix (examining difference in thickness after controlling for effects of age,

Re: [Freesurfer] mri_glmfit error

That terminal output asks you to send 4 things, but you only sent 2 On 9/29/2022 11:51 AM, fernanda rohrsetzer wrote: External Email - Use Caution Hi, I attempted to execute mri_glmfit on my structural data through the following command - mri_glmfit --y lh.10.teste.thickness.mgh --fs

[Freesurfer] mri_glmfit error

External Email - Use Caution Hi, I attempted to execute mri_glmfit on my structural data through the following command - mri_glmfit --y lh.10.teste.thickness.mgh --fsgd testCT.fsgd --C Contrasts/LR-HR_testcov.mtx --C Contrasts/LR-MDD_testcov.mtx --C Contrasts/HR-MDD_testcov.mtx

Re: [Freesurfer] mri_glmfit error: MatrixResidualForming(): X is not invertable

: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit error: MatrixResidualForming(): X is not invertable ⚠ Caution: External sender My guess is that the variable (G_cingul vol) should be normalized (remove the mean and divide by the stddev). On 9/6/2022 5:44 PM, Piot

Re: [Freesurfer] mri_glmfit error: MatrixResidualForming(): X is not invertable

My guess is that the variable (G_cingul vol) should be normalized (remove the mean and divide by the stddev). On 9/6/2022 5:44 PM, Piot, Alex wrote: External Email - Use Caution Hello Freesurfer experts, I am trying to perform a GLM, using the volume of a brain region as a covariate

[Freesurfer] mri_glmfit error: MatrixResidualForming(): X is not invertable

External Email - Use Caution Hello Freesurfer experts, I am trying to perform a GLM, using the volume of a brain region as a covariate. I am doing a two-group, one covariate design. I originally tried to use QDEC to facilitate the process and received an error message that the

Re: [Freesurfer] mri_glmfit error

You don't have enough members in the classes to fit the model that you have. Eg, class d has 4 members with which you are fitting an offset and 3 slopes leaving you with 0 degrees of freedom. You need to get more subjects or change your model. btw, gender is usually modeled as a discrete rather

[Freesurfer] mri_glmfit error

External Email - Use Caution Hello FreeSurfer Developers, my fsgd is this： GroupDescriptorFile 1 Title post compane Class d Class m Class h RescaleFlag 1 DemeanFlag 1 Variables gender Age Edu Input bd1 d 0 15 8 Input bd2 d 1 19 13 Input bd7 d 0 17 11 Input bd8 d 1 19 13 Input bd6

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

External Email - Use Caution Hi Dr. Greve, Thank you very much for your solution. That solved the problem. I genuinely appreciate your support! Best, Hyunwoo Jeong 2022년 3월 10일 (목) 오전 2:52, Douglas N. Greve 님이 작성: > The problem is that your design matrix is badly scaled. The e

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

The problem is that your design matrix is badly scaled. The eTIV values are much larger than the group membership (value=1). Try subtracting the mean of the eTIV and dividing by the stddev to normalize it. On 2/25/2022 8:07 PM, 정현우 wrote: External Email - Use Caution Hi Dr. Greve,

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

External Email - Use Caution Hi Dr. Greve, Thank you for your response. I uploaded the .mgh, .fsgd, and .mtx files that I used to run the mri_glmfit command. I can upload the recon-all outputs of the individual samples as well, if needed. The files are uploaded in google drive, pl

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

Can you upload the data to me somewhere? I'd need the input volume and the fsgd and any contrasts On 2/21/2022 10:24 PM, 정현우 wrote: External Email - Use Caution Hi Dr. Greve, Thank you for your suggestion. Unfortunately, the same problem occurred when I ran the command with --no-pcc

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

External Email - Use Caution Hi Dr. Greve, Thank you for your suggestion. Unfortunately, the same problem occurred when I ran the command with --no-pcc. Folders and files with the same names were created. and the following error message (identical to the previous one) appeared. e

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

External Email - Use Caution Hi Dr. Greve, Thank you for your suggestion. Unfortunately, the same problem occurred when I ran the command with --no-pcc. Folders and files with the same names were created. and the following error message (identical to the previous one) appeared. e

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

External Email - Use Caution Hi Dr. Greve, Thank you for your suggestion. Unfortunately, the same problem occurred when I ran the command with --no-pcc. Folders and files with the same names were created. and the following error message (identical to the previous one) appeared. e

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

It looks like it is failing when computing the partial correlation coef. Try  running it with --no-pcc On 2/16/2022 10:53 AM, 정현우 wrote: External Email - Use Caution Hi Dr. Greve, Yes, it seems like the output folder and some output files were created. After running the mri_glmfit,

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

External Email - Use Caution Hi Dr. Greve, Yes, it seems like the output folder and some output files were created. After running the mri_glmfit, 'three_group_comparison.area.lh.glmdir' folder was created. In the glmdir folder, 'three_group_comparison.area' folder was created, an

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

Did it create the output folder and some output files? I noticed that there is a "error: No such file or directory" error On 2/14/2022 8:46 PM, 정현우 wrote: External Email - Use Caution Hi Dr. Greve, Thank you for your reply. I attached the fsgd file, mtx file and the Xg.dat file

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

External Email - Use Caution Hi Dr. Greve, Thank you for your reply. I attached the fsgd file, mtx file and the Xg.dat file below. Hyunwoo Jeong 2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve 님이 작성: > can you send your fsgd file and the Xg.dat file? > > On 2/14/2022 1:21 AM, 정현우 wr

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

can you send your fsgd file and the Xg.dat file? On 2/14/2022 1:21 AM, 정현우 wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare cortical surface area among three groups while controlling for estimated total intracranial volume (eTIV), as describ

[Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare cortical surface area among three groups while controlling for estimated total intracranial volume (eTIV), as described on the Surface Based Group Analysis tutorial ( https://secure-web.cisco.com/1

Re: [Freesurfer] mri_glmfit error

The format is not correct. It should be Input SubjectID Class You have SubjectID in there twice On 4/1/2021 1:15 AM, Ishi Tandon AIB, Jaipur wrote: External Email - Use Caution Hello FS experts, I attempted to execute  mri_glmfit on my structural data through the following command -

[Freesurfer] mri_glmfit error

External Email - Use Caution Hello FS experts, I attempted to execute mri_glmfit on my structural data through the following command - mri_glmfit --y final.lh.mTBI.volume.10.mgh --fsgd FSGD/mild.tbi.fsgd dods -C contrats/HC-mTBI.mtx --surf fsaverage --cortex --glmdir lh.volume.g

Re: [Freesurfer] mri_glmfit error

Can you send the full terminal output? On 6/15/2020 10:41 PM, 邓刊 wrote: External Email - Use Caution Hello Freesurfer Experts! I met the mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08.I am trying to run a 8 group 3 variables analysis: with diagnosis bei

[Freesurfer] mri_glmfit error

External Email - Use Caution Hello Freesurfer Experts! I met the mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08.I am trying to run a 8 group 3 variables analysis: with diagnosis being my variable of interest and trying to regress out the effects of

Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

This is a design problem that will not be solved by simply forcing glmfit to run. I would remove that class and those subjectgs On 5/13/2020 2:33 PM, Marina Fernández wrote: External Email - Use Caution Thank you, Doug. That makes sense. Do you think in this case it is a good option

Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

External Email - Use Caution Thank you, Doug. That makes sense. Do you think in this case it is a good option to add the flag --illcond to run this analysis without getting an error? or is it better not to use the variable apoe in these statistical analyzes? What do you recommend

Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

The problem is that class 3 (smaleapoe) only has two members but you have four covariates. When you use DODS, each class gets its own fit to the data. In this case, class 3 is trying to solve for 5 unkowns (offset + 4 slopes) with only two data points. On 5/13/2020 10:18 AM, Marina Fernández w

Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

External Email - Use Caution Hi Douglas, I email you the fsgd file and I have also sent it through FTP. Thank you for your attention. Best regards, Marina. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh

Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

Can you email the fsgd file? On 5/12/2020 1:35 PM, Marina Fernández wrote: External Email - Use Caution Dear Freesurfer experts, I get the error that you can find at the end of this message when I am running mri_glmfit. Whenever I run an analysis in which the experimental design ha

[Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

External Email - Use Caution Dear Freesurfer experts, I get the error that you can find at the end of this message when I am running mri_glmfit. Whenever I run an analysis in which the experimental design has more than 12 columns, I get the same error, whereas if the experimental

[Freesurfer] mri_glmfit error

External Email - Use Caution Dear Freesurfer experts, I get the error that you can find at the end of this message when I am running mri_glmfit. Whenever I run an analysis in which the experimental design has more than 12 columns, I get the same error, whereas if the experimenta

Re: [Freesurfer] mri_glmfit error

Did you see the part where it says "If you seek help with this problem, make sure to send:"? On 9/5/2019 11:00 PM, Gwang-Won Kim wrote: External Email - Use Caution Hi there, I tried to analysed "mri_glmfit --glmdir g1v7.wls --y ces.nii.gz --wls cesvar.nii.gz --C Main.mtx --C PDI.mtx

[Freesurfer] mri_glmfit error

External Email - Use CautionHi there, I tried to analysed "mri_glmfit --glmdir g1v7.wls --y ces.nii.gz --wls cesvar.nii.gz --C Main.mtx --C PDI.mtx --C Sex.mtx --C Age.mtx --C Edu.mtx --C BDI.mtx --C SBQ.mtx --C CD.mtx --fsgd g1v7.fsgd --surface fsaverage lh --cortex --fwhm 5 " Ther

Re: [Freesurfer] mri_glmfit ERROR no voxels found

There should not be any rounding in mris_preproc, so I don't know why it is behaving in that way. On 06/08/2018 05:12 AM, Marine Boudot de la Motte wrote: > > > Dear Douglas, > > Thank you very much for your answer. > Actually, I looked a little bit deeper into the problem, and found out > that

Re: [Freesurfer] mri_glmfit ERROR no voxels found

External Email - Use Caution Dear Douglas, Thank you very much for your answer. Actually, I looked a little bit deeper into the problem, and found out that when I project the MTR of each subject on the surface, all my MTR values are correct and well projected. But once I run mris_

Re: [Freesurfer] mri_glmfit ERROR no voxels found

By default, mri_glmfit will exclude any voxels where there is even a single data point that is 0. It looks like all your voxels fall into that category. If this is really ok and you want to analyze voxels where some data points are 0, then add --no-prune. On 6/6/18 4:12 PM, Marine Boudot de l

[Freesurfer] mri_glmfit ERROR no voxels found

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to do a Surface-based analysis on Freesurfer while projecting MTR MRI sequences. I have followed all the steps explained in the group analysis tutorials, and the mri_preproc seems to have ran correctly but on

Re: [Freesurfer] mri_glmfit ERROR: loading gamma0

Can you send me the mtx file? On 1/11/18 3:08 AM, Gemma Salvadó Blasco wrote: Hi Douglas, yes, the file exists and I have read permissions. Is there any file (.log, error,...?) that could you help to understand where the problem is? Thank you, Gemma On 10 January 2018 at 00:07, Douglas N

Re: [Freesurfer] mri_glmfit ERROR: loading gamma0

Hi Douglas, yes, the file exists and I have read permissions. Is there any file (.log, error,...?) that could you help to understand where the problem is? Thank you, Gemma On 10 January 2018 at 00:07, Douglas N Greve wrote: > does this file exist and do you have read permissions? > > /home/gs

Re: [Freesurfer] mri_glmfit ERROR: loading gamma0

does this file exist and do you have read permissions? /home/gsalvado/Projects/Amyloid_Staging/Data/FreeSurfer/Stage0-stage1NoSex.intercept.mtx On 01/09/2018 09:34 AM, Gemma Salvadó Blasco wrote: > Hello Freesurfer developers, > I'm make a statistical analysis between two groups. To do this,

[Freesurfer] mri_glmfit ERROR: loading gamma0

Hello Freesurfer developers, I'm make a statistical analysis between two groups. To do this, I followed the instructions of the Fs tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) but I'm having a problem at the last step of the process (mri_glmfit). I've checked that

Re: [Freesurfer] mri_glmfit error (mri_reshape number of elements)

not sure what is going wrong. Does it work if you do not include the --wls cesvar.nii.gz ? On 6/28/17 12:29 PM, Mcnorgan, Christopher wrote: Hi, I’m running a group-level analysis and have encountered an error that results in a core dump. The first-level analyses were run using the fsaverage

[Freesurfer] mri_glmfit error (mri_reshape number of elements)

Hi, I’m running a group-level analysis and have encountered an error that results in a core dump. The first-level analyses were run using the fsaverage surfaces, rather than self surfaces. I’ve already inspected the individual contrasts, loading the fsaverage surface in tksurfer and rendering ea

Re: [Freesurfer] mri_glmfit error with aparc table flag

> > > post in the > > > > >> forum that used "--surf fsaverage lh "‎ > and it > > worked. > > > > >> Best, > > > > >> Paul > >

Re: [Freesurfer] mri_glmfit error with aparc table flag

lt;mailto:miracoo...@gmail.com> > > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>>> wrote: > > > > >> Thanks doug. Does it mean when using the --table > > > flag, you > > > > can't &

Re: [Freesurfer] mri_glmfit error with aparc table flag

me across several > > post in the > > > >> forum that used "--surf fsaverage lh "‎ and it > worked. > > > >> Best, > > > >> Paul > > > >> > > > >>

Re: [Freesurfer] mri_glmfit error with aparc table flag

e fsaverage template? I came across several > > post in the > > > >> forum that used "--surf fsaverage lh "‎ and it worked. > > > >> Best, > > > >> Paul > >

Re: [Freesurfer] mri_glmfit error with aparc table flag

Best, > > >> Paul > > >> > > >> Sent from my BlackBerry 10 smartphone. > > >> *From: *Douglas Greve > > >> *Sent: *Tuesday, April 18, 2017 9:52 PM > > >> *To: *free

Re: [Freesurfer] mri_glmfit error with aparc table flag

ked. > > >> Best, > > >> Paul > > >> > > >> Sent from my BlackBerry 10 smartphone. > > >> *From: *Douglas Greve > > >> *Sent: *Tuesday, April 18, 2017 9:52 PM > > >> *To: *frees

Re: [Freesurfer] mri_glmfit error with aparc table flag

as Greve > >> *Sent: *Tuesday, April 18, 2017 9:52 PM > >> *To: *freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > >> <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>&g

Re: [Freesurfer] mri_glmfit error with aparc table flag

y BlackBerry 10 smartphone. > >> *From: *Douglas Greve > >> *Sent: *Tuesday, April 18, 2017 9:52 PM > >> *To: *freesurfer@nmr.mgh.harvard.edu > >> <mailto:freesurfer@nmr.mgh.harvard.edu> > >> *Reply To: *Freesurfer support list > >&

Re: [Freesurfer] mri_glmfit error with aparc table flag

t used "--surf fsaverage lh "‎ and it worked. >> Best, >> Paul >> >> Sent from my BlackBerry 10 smartphone. >> *From: *Douglas Greve >> *Sent: *Tuesday, April 18, 2017 9:52 PM >> *To: *freesurfer@nmr.mgh.harvard.edu >

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] mri_glmfit error with aparc table flag

lh "‎ and it worked. > Best, > Paul > > Sent from my BlackBerry 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 erro

Re: [Freesurfer] mri_glmfit error with aparc table flag

Re: [Freesurfer] mri_glmfit error 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.txt co

Re: [Freesurfer] mri_glmfit error with aparc table flag

esday, April 18, 2017 9:52 PMTo: freesurfer@nmr.mgh.harvard.eduReply To: Freesurfer support listSubject: Re: [Freesurfer] mri_glmfit error with aparc table flag Don't include --surf fsaverage lh. It thinks the input is a surface, not a table On 4/18

Re: [Freesurfer] mri_glmfit error 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.txt contain entorhinal and parahippocampal thickness values for 32 subje

[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

I can't tell from the glmfit command line what you are trying to do. Generally, the GLM is run on group data and you specify an average brain (eg, fsaverage) as the --surf. On 07/14/2016 06:10 AM, Chatzi, Vasiliki wrote: > > > Dear Developers, > > > I am trying to run the mri_glmfit command and

Re: [Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

It does not look like the variables are demeaned (your FSGD file below) Variables Age eTIV EnglishParityRT Input Math_5001m Monolingual_male 18 1865790.30866 -8952.208 Input Math_5002m Monolingual_female 19 1520429.68796 -4605.208 Input Math_5003m Monolingual_male 19 1749716.72939

Re: [Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

Hi Doug, Thank you for your response. The current fsgd file I sent you was with the covariates demeaned x 100, as I saw you recommend that to someone else. We previously tried doing just the demeaned values without multiplying by 100, and that still had the badly scaled error. Do you think we s

Re: [Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

This is almost surely a problem with scaling as your covariates are huge. Try subtracting the mean and dividing by the stddev before entering into the FSGD file. Compute the means and stddevs across all subjects. doug On 07/11/2016 03:20 PM, Jennifer Legault wrote: > Hi Freesurfer Experts, > >

[Freesurfer] mri_glmfit error

Dear Developers, I am trying to run the mri_glmfit command and I get two different errors for two different subjects. Please find details below. I would be really grateful if you could provide any advice. Error1 setenv SUBJECTS_DIR ./ mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_t

[Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

Hi Freesurfer Experts, I am trying to run mri_glmfit and while 90% of my files work, some of them display the error below. I have tried demeaning, and then tried multiplying this value by 100, and I still get the same error. Any feedback would be greatly appreciated. mris_preproc done srcsubjec

Re: [Freesurfer] mri_glmfit error " FSGD file exceeds the maximum allowed 2000"

This is hard coded unfortunately. I've bumped it up to 20k in the most recent version. I've put a linux version here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit On 03/16/2015 06:38 AM, Avram Holmes wrote: > FreeSurfer List, > > I am attempting to run an analyses o

[Freesurfer] mri_glmfit error " FSGD file exceeds the maximum allowed 2000"

FreeSurfer List, I am attempting to run an analyses on 2051 participants. However, when I reach the mri_glmfit stage I receive the following error. ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum allowed 2000 Is there a work around for this? Thank you in advance for

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

Thank you Doug! I replaced all my spaces with new spaces and it worked! Much appreciated! Lindsay On Fri, Dec 12, 2014 at 12:09 PM, lindsay hanford wrote: > > Hi Doug! > > Thank you very much for your reply. I made the fsgd file in a plain-text > file using the textedit program on a Mac and when

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

The file I looked at had a bunch of carriage returns (try looking at it with more or less or cat). As long as those are in there, it will create an error. Try running this and using the new one cat g4v1.73.fsgd | sed 's/\r/\n/g' > new.g4v1.73.fsgd On 12/12/2014 12:09 PM, lindsay hanford wrote:

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

Hi Doug! Thank you very much for your reply. I made the fsgd file in a plain-text file using the textedit program on a Mac and when that didn't work I tried modifying in the terminal window using: nano -w g4v1.73.fsgd. This also didn't solve the problem. I am not sure what to try next. Lindsay O

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

Your FSGD file appears to have been made under windows or using an editor that is not simple text. The contrast matrix looks ok. doug On 12/01/2014 02:41 PM, lindsay hanford wrote: > Hello Freesurfer Experts! > > I am encountering the dreaded mri_glmfit error: matrix is > ill-conditioned or b

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

Hello, Has anyone had a chance to look at this? I still haven't been able to solve the problem. Thanks! Lindsay On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford wrote: > Hello Freesurfer Experts! > > I am encountering the dreaded mri_glmfit error: matrix is ill-conditioned > or badly scaled, c

Re: [Freesurfer] mri_glmfit error

Thanks Douglas. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au

Re: [Freesurfer] mri_glmfit error

You have a --C that is not followed by a contrast file. doug On 11/26/14 10:58 PM, Bronwyn Overs wrote: Dear Freesurfer Mailing list, I have been attempting to run the following command in freesurfer v5.3.0: mri_glmfit --y site-gender-group-prothaplotype.thick.lh.10.mgh --fsgd site-gender-gr

[Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

Hello Freesurfer Experts! I am encountering the dreaded mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08. I have tried to troubleshoot how to solve this problem from other inquiries, however, I still have had no luck. I am trying to run a 4 group 1 variable analysis: wi

[Freesurfer] mri_glmfit error

Dear Freesurfer Mailing list, I have been attempting to run the following command in freesurfer v5.3.0: mri_glmfit --y site-gender-group-prothaplotype.thick.lh.10.mgh --fsgd site-gender-group-prothaplotype.fsgd dods --C me_site-BrisVsMelb.mtx --C me_site-BrisVsPer.mtx --C me_site-MelbVsPer.mtx

Re: [Freesurfer] mri_glmfit error

Hi Doug and others, Thanks Doug. All the best. 2013-12-20 Rujing Zha 发件人：Douglas N Greve 发送时间：2013-12-20 00:11 主题：Re: [Freesurfer] mri_glmfit error 收件人："Rujing Zha" 抄送："freesurfer" On 12/18/2013 11:14 PM, Rujing Zha wrote: > Hi Doug and others, > Thanks Doug.

Re: [Freesurfer] mri_glmfit error

correct? Yes > Thanks. > All the best. > 2013-12-19 > > /Rujing Zha/ > ---- > *发件人：*Douglas Greve > *发送时间：*2013-12-19 11:34 > *主题：*Re: [Freesurfer] mri_glmfit error > *收件人：*"Rujing Zha" > *抄送

Re: [Freesurfer] mri_glmfit error

. Is this correct? Thanks. All the best. 2013-12-19 Rujing Zha 发件人：Douglas Greve 发送时间：2013-12-19 11:34 主题：Re: [Freesurfer] mri_glmfit error 收件人："Rujing Zha" 抄送："freesurfer" On 12/18/13 10:26 PM, Rujing Zha wrote: Hi Doug and others, Thanks Doug. I modifiled my number

Re: [Freesurfer] mri_glmfit error

. 2013-12-19 /Rujing Zha/ *发件人：*Douglas N Greve *发送时间：*2013-12-19 04:59 *主题：*Re: [Freesurfer] mri_glmfit error *收件人：*"freesurfer" *抄送：* Could

Re: [Freesurfer] mri_glmfit error

distinguish which subject is female or male in each class if dividing all subjects into 2 classes (i.e con and IA )? Thanks in advance. All the best. 2013-12-19 Rujing Zha 发件人：Douglas N Greve 发送时间：2013-12-19 04:59 主题：Re: [Freesurfer] mri_glmfit error 收件人："freesurfer" 抄送： Could be seve

Re: [Freesurfer] mri_glmfit error

Could be several things. You only have two IA_female and and only 3 con_female. Also, the age and edu are highly correlated. I would try creating a single IA group with males and females and a single con group doug On 12/18/2013 11:21 AM, Rujing Zha wrote: > Hi all, > I try to run mri_glmfit,

[Freesurfer] mri_glmfit error

Hi all, I try to run mri_glmfit, but it export "ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.". I upload the data

Re: [Freesurfer] mri_glmfit error: negative DOF -10

It usually means that the number of subjects in the input is less (10 less) than the number of regressors. It looks like you have about 14 input subjects and 24=6*4 regressors. You need to add subjects or remove regressors (ie, classes or covariates) doug On 9/18/13 11:41 AM, Robert Schulz wro

[Freesurfer] mri_glmfit error: negative DOF -10

Hello, I am using mri_glmfit to perform a correlation analysis between some surface-based DTI measures and a behavioural outcome (grip), aiming to correct for scannertyp (C,I,W), handedness (R,L) as discrete variables and age (AGE) and duration (Mo) as continuous covariates. Please find the fsg

Re: [Freesurfer] mri_glmfit error with design matix

Hi sinead, you only have one TGMale. You can't fit aslope and intercept to a single point! doug On 05/15/2013 11:40 AM, Sinead Kelly wrote: > Dear Members, > > I am using mri_glmfit for the first time with the .fsgd file below, > however, I am receiving the following error: ERROR: matrix is >

[Freesurfer] mri_glmfit error with design matix

Dear Members, I am using mri_glmfit for the first time with the .fsgd file below, however, I am receiving the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries an

[Freesurfer] mri_glmfit error

HI, I am trying to see difference in groupmap between 2 time-point within 1 group with glmfit. I followed the instruction"PairedAnalysis". mris_preproc --paired-diff mri_glmfit --surf fsaverage "$hemi" --y "$hemi"_cope1_"$grp".sm"$fwhmsrc".mgh --yffxvar "$hemi"_varcope1_"$grp".sm"$fwhmsrc".m

[Freesurfer] mri_glmfit error

Hi Freesurfers, I am having problems with mri_glmfit. I am doing a one sample ttest with thickness values. However, when i enter "-surf Subject1 lh thickness.fsaverage.mgh", I receive an error message saying that the surface could not be opened. The path is correct and I entered "setenv SUBJECT

[Freesurfer] Mri_glmfit ERROR: dimension inconsistency in source data

Hi, During running fixed effects glm to combine runs, the analysis of all but one subject went fine. The log file contains this error message: mri_surf2surf --srcsubject 1250 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval 3runs/tmp.mris_prep

Re: [Freesurfer] mri_glmfit error

That command would be for an mc-z simlation, not a permutation. But you are right the perm does not allow non-orthogonal matrices. The mc-z synthesizes a z-field, smooths it, thresholds it, and extracts clusters, repeats this 1 times to get an idea of what cluster sizes should be expected u

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