Re: [Freesurfer] selxavg3-sess out of memory error

You can try running mri_glmfit to run a fixed effects analysis fist, concatenate all the ces.nii.gz files (mri_concat */ces.nii.gz --o all.ces.nii.gz) second, do the same for the cesvar.nii.gz files third, compute total dof (see the dof.dat files in each run folder) 4th, mri_glmfit --y

Re: [Freesurfer] selxavg3-sess out of memory error

External Email - Use Caution Hi Doug, thanks for the advice! I can compute the GLM and contrasts per run. But selxavg3 does not compute contrasts across the runs with per-run. Could you give me some advice on how to concatenate the per run contrasts - can I just append them and

Re: [Freesurfer] selxavg3-sess out of memory error

Sorry, I thought I sent an email responding to this. Try running it with -run-wise. This will analyze each run separately. I can't remember whether it generates a final combined average (been a long time since I used this option), but run it and see what it does. On 6/23/2022 2:00 PM, Caspar

Re: [Freesurfer] selxavg3-sess out of memory error

External Email - Use Caution Hi! Any advice on this issue? The error message is: Starting contrasts UrInv J=1 - Out of memory. Type "help memory" for your options. Error in fast_glm_pcc (line 39) yhatd = Rd*(X*beta); Error in fast_fratiow (line 136) if(nargout

[Freesurfer] selxavg3-sess out of memory error

External Email - Use Caution Hi! I am running large single subject GLMs with selxavg3-sess and I run into a Matlab "out of memory" error. I was wondering whether you had any advice on how to get around that. I have 40-50 runs per subject, and the analyses are whole brain. The GLM

Re: [Freesurfer] selxavg3-sess not working

I don't understand what the problem is. There is no error in the log file. If you want to redo the  preprocessing, you should rerun preproc-sess with the -force flag On 3/20/2020 12:25 PM, Nasiriavanaki, Zahra wrote: Hi Doug Thanks for your reply. Unfortunately I am still having problem.

Re: [Freesurfer] selxavg3-sess not working

.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer selxavg3-sess-bold-loom.lh-200320115858.log Descriptio

Re: [Freesurfer] selxavg3-sess not working

oh, sorry, I misread your earlier email. The -force in selxavg3-sess only applies to the post processing. If  you want to redo the preprocessing, then run preproc-sess -force On 3/13/2020 7:28 PM, Nasiriavanaki, Zahra wrote: Hi Doug Thanks for your reply. Yes, I did. I run the command from

Re: [Freesurfer] selxavg3-sess not working

Hi Doug Thanks for your reply. Yes, I did. I run the command from the folder where my analysis which I call loom.lh is located. selxavg3-sess -s $subj -d ../all_subjects -analysis loom.lh -force On Mar 13, 2020, at 6:41 PM, Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: Did you

Re: [Freesurfer] selxavg3-sess not working

Did you pass it an analysis? There is not one in that command line On 3/12/2020 11:28 AM, Nasiriavanaki, Zahra wrote: Hi Freesurferers I am trying to run selxavg3-sess for a single subject (3T fMRI data). Oddly, the  terminal output shows that it doesn't need updating for preprocessing and

[Freesurfer] selxavg3-sess not working

Hi Freesurferers I am trying to run selxavg3-sess for a single subject (3T fMRI data). Oddly, the terminal output shows that it doesn't need updating for preprocessing and ends with this: "Started at Thu Mar 12 10:48:09 EDT 2020 Ended at Thu Mar 12 10:48:12 EDT 2020 preproc-sess done". It

[Freesurfer] selxavg3-sess design ill-conditioned

External Email - Use Caution Hello, I'm analyzing retinotopy data. I used expanding ring and rotating wedge. For my pilot, unfortunately, we used only 2 cycles for each stimulus and 1 cycle lasted 200 seconds (for sure I will change to more cycles lasting less). TR = 2.5.

Re: [Freesurfer] selxavg3-sess

It is having some problems unzipping a nifti file. Does it work on other runs/sessions/subjects? If so, then there might be something wrong with that file. Alternative, check /var/volders/v3 to see if the disk is filling up. On 10/1/2019 1:43 PM, Sanati Monfared, Shamsi wrote: External

[Freesurfer] selxavg3-sess

External Email - Use Caution Hi all, I am running the functional analyses (selxavg3_sess) and stuck at the following error, which I have no idea what to do (apparently the analyses have been OK up until run 010 and the error happened in run 012). I received the same errors in

Re: [Freesurfer] selxavg3-sess failed

It does not look like the error was captured in the log file. Can you send the full terminal output? On 6/2/2019 5:02 AM, starxifd wrote: External Email - Use CautionIt Hi, FS experts I got into trouble when running ’selxavg3-sess’ with a session id file. All sessions

Re: [Freesurfer] freesurfer selxavg3-sess error

Can you include the command line and full terminal output? From what you have below, it says it is only finding one non-null condition, so double check your par files On 11/12/2018 04:58 PM, Francesca Strappini wrote: > > External Email - Use Caution > > Thank you! > I changed the event

Re: [Freesurfer] freesurfer selxavg3-sess error

External Email - Use Caution Thank you! I changed the event file and re-run the analysis. I got an error message when creating the contrast: mkanalysis-sess -analysis FF-MonkeyCassis-event.sm03.lh -surface MonkeyCassis lh -fwhm 3 -fsd bold -per-run -event-related -paradigm FF.par

Re: [Freesurfer] freesurfer selxavg3-sess error

When you ran mkanalysis-sess, did you specify two event types? You only have one non-null event in your paradigm file. On 10/28/2018 08:57 AM, Francesca Strappini wrote: > > External Email - Use Caution > > Thanks! Now it's loading correctly my event file. > However, when I run

Re: [Freesurfer] freesurfer selxavg3-sess error

External Email - Use Caution Thanks! Now it's loading correctly my event file. However, when I run selxavg3-sess I get this error message: selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF -no-con-ok outanadir =

Re: [Freesurfer] selxavg3-sess contrasts error

External Email - Use Caution Thank you! It was a format problem. Best Francesca Il giorno mer 22 ago 2018 alle ore 17:51 Douglas N. Greve < dgr...@mgh.harvard.edu> ha scritto: > There is something wrong with the paradigm file (-par when running > mkanalysis-sess). Check the

Re: [Freesurfer] selxavg3-sess contrasts error

There is something wrong with the paradigm file (-par when running mkanalysis-sess). Check the paradigm file for this subject and run. On 08/22/2018 10:16 AM, Francesca Strappini wrote: > > External Email - Use Caution > > Hi, > > I'm trying to analyze a block-design experiment. I run

[Freesurfer] selxavg3-sess contrasts error

External Email - Use Caution Hi, I'm trying to analyze a block-design experiment. I run selxavg3-sess: selxavg3-sess -s MS -analysis MS_VisLocDrawings.sm03.rh And I got this error message while computing the contrasts. Any idea what does it mean? outtop =

Re: [Freesurfer] selxavg3-sess /tmp dir out of space

oh, that functionality is only available in 6.0. In 5.3, the temp path is hard-coded. You can edit load_nifti.m to change the default path. On 6/6/18 6:36 AM, Jiahe Zhang wrote: External Email - Use Caution /usr/local/freesurfer/stable5_3_0/bin/freesurfer On Wed, Jun 6, 2018 at

Re: [Freesurfer] selxavg3-sess /tmp dir out of space

External Email - Use Caution /usr/local/freesurfer/stable5_3_0/bin/freesurfer On Wed, Jun 6, 2018 at 12:23 AM, Douglas Greve wrote: > what version of fs are you running? > > On 6/5/18 10:02 PM, Jiahe Zhang wrote: > > External Email - Use Caution > I tried both below and

Re: [Freesurfer] selxavg3-sess /tmp dir out of space

what version of fs are you running? On 6/5/18 10:02 PM, Jiahe Zhang wrote: External Email - Use Caution I tried both below and got the same error. setenv TMPDIR $my_tmp_dir setenv tmpdir $my_tmp_dir Is doesn't seems like selxavg3-sess reads this env variable. Or am I missing

Re: [Freesurfer] selxavg3-sess /tmp dir out of space

External Email - Use Caution I tried both below and got the same error. setenv TMPDIR $my_tmp_dir setenv tmpdir $my_tmp_dir Is doesn't seems like selxavg3-sess reads this env variable. Or am I missing something? On Mon, Jun 4, 2018 at 5:56 PM, Douglas N. Greve wrote: > > set

Re: [Freesurfer] selxavg3-sess /tmp dir out of space

set the TMPDIR env variable to point anywhere you want On 06/04/2018 02:57 PM, Jiahe Zhang wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > While running selxavg3-sess on a large functional scan (7 Tesla, 768 > time points), I got these errors > > gzip: stdout:

[Freesurfer] selxavg3-sess /tmp dir out of space

External Email - Use Caution Dear Freesurfer experts, While running selxavg3-sess on a large functional scan (7 Tesla, 768 time points), I got these errors gzip: stdout: No space left on device ERROR: /tmp/tmp8187256.nii, read in 1669519272 voxels, expected 3257077248 It sounds

Re: [Freesurfer] freesurfer selxavg3-sess error

oops, sorry. Looks like it is having a problem loading your paradigm file. Check that. If the error does not pop out to you then send it to me. On 05/02/2018 10:06 AM, Francesca Strappini wrote: > Hi, sorry, maybe my last email got lost. Is there anything I can try > to fix this problem with

Re: [Freesurfer] freesurfer selxavg3-sess error

External Email - Use Caution Hi, sorry, maybe my last email got lost. Is there anything I can try to fix this problem with selxavg3-sess? Thanks! Best Francesca 2018-04-24 20:35 GMT+03:00 Francesca Strappini : > Thank you for the reply! > I

Re: [Freesurfer] freesurfer selxavg3-sess error

External Email - Use Caution Thank you for the reply! I deleted the contrasts and run this command line: selxavg3-sess -a FF-MonkeyCassis.sm03.rh -s MonkeyCassis-FF -no-con-ok --- matlab output MATLAB is selecting SOFTWARE OPENGL rendering.

Re: [Freesurfer] freesurfer selxavg3-sess error

Try deleting the contrasts (.mat files) and rerunning On 4/24/18 5:48 AM, Francesca Strappini wrote: Dear FreeSurfer experts, I'm trying to analyze some monkey functional data. I got this error message with selxavg3-sess. I run the following commands: mkcontrast-sess -analysis

[Freesurfer] freesurfer selxavg3-sess error

External Email - Use Caution Dear FreeSurfer experts, I'm trying to analyze some monkey functional data. I got this error message with selxavg3-sess. I run the following commands: mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast ON-vs-OFF -a 1 -c 0 mkcontrast-sess

Re: [Freesurfer] selxavg3-sess problem: SVD input matrix contains NaN

An epiphany lead me to the solution to the problem, which I shall post here since I am apparently due to experience it again in 2019. The NAN values in the GLM matrices were the result of there being a condition that did not appear in any of the .par files across all of the runs. Once these

Re: [Freesurfer] selxavg3-sess error

not sure what is going on. Is the script stem2fname in your path? If so, run selxavg3-sess with -debug as the first option and send the terminal output On 5/16/17 3:08 AM, std...@virgilio.it wrote: Hi list, this error occurs during selxavg3-sess in FS-FAST fcMRI meanval --i stem2fname stem

[Freesurfer] selxavg3-sess error

Hi list, this error occurs during selxavg3-sess in FS-FAST fcMRI meanval --i stem2fname stem Looks for stem.fmt where fmt is mgh mgz nii nii.gz bhdr img w, then returns stem.fmt. See also stem2fmt, fname2stem The file needs to exist on disk. --m 001/masks/brain.e3.nii.gz --o

Re: [Freesurfer] Selxavg3-sess Looking for (and can't find) "fmc.sm0"

can you send the full terminal output? On 04/05/2017 04:02 PM, Taylor, Johnmark wrote: > Hello, > > I am getting an odd bug on selxavg3-sess. I am getting the error message, > > *ERROR: cannot find [rest of file path]/fmc.sm0* > > I am indicating zero smoothing in mkanalysis-sess ("-fwhm 0"). I

[Freesurfer] Selxavg3-sess Looking for (and can't find) "fmc.sm0"

Hello, I am getting an odd bug on selxavg3-sess. I am getting the error message, *ERROR: cannot find [rest of file path]/fmc.sm0* I am indicating zero smoothing in mkanalysis-sess ("-fwhm 0"). I am confused because the output of preproc-sess for no smoothing is fmc.nii.gz, *NOT *fmc.sm0.nii.gz

Re: [Freesurfer] selxavg3-sess: F-contrast but multiple dimension in sig

if you used the identity matrix then it is the first one On 02/08/2017 08:43 AM, Seung-Goo KIM wrote: > Thank you very much, Doug, > > One more question: so the sig have all T-test results of contrasts > like [1 0 0 … 0], [0 1 0 ... 0], …, [0 0 0 … 1], right? or [1 -1/(N-1) > -1/(N-1), …

Re: [Freesurfer] selxavg3-sess: F-contrast but multiple dimension in sig

Thank you very much, Doug, One more question: so the sig have all T-test results of contrasts like [1 0 0 … 0], [0 1 0 ... 0], …, [0 0 0 … 1], right? or [1 -1/(N-1) -1/(N-1), … -1/(N-1)] ? Best, -- Seung-Goo KIM > On 2017-02-06, at 18:54, Douglas N Greve wrote: >

Re: [Freesurfer] selxavg3-sess: F-contrast but multiple dimension in sig

yes, fsig is the F test. The sig has the result of all the individual t-tests On 02/06/2017 08:41 AM, Seung-Goo KIM wrote: > Dear surfers, > > I computed F-contrast using selxavg3-sess with an identity matrix as a > contrast matrix. My question is about the result file “sig.*”. As far > as I

[Freesurfer] selxavg3-sess: F-contrast but multiple dimension in sig

Dear surfers, I computed F-contrast using selxavg3-sess with an identity matrix as a contrast matrix. My question is about the result file “sig.*”. As far as I understand, the “sig.*” file contains signed-minnus-log-p-values (like, -log10(p)*Sign(t)) for a certain contrast. So I expected the

Re: [Freesurfer] selxavg3-sess error

Thank you, I'll try! Best Francesca On Wednesday, June 15, 2016, Douglas N Greve wrote: > Sorry for the delay. Do you have polar angle data? Unfortunately, FSFAST > needs both. If you don't have polar, just copy the eccen data and call > it polar. for what you want

Re: [Freesurfer] selxavg3-sess error

Sorry for the delay. Do you have polar angle data? Unfortunately, FSFAST needs both. If you don't have polar, just copy the eccen data and call it polar. for what you want to do it won't make much difference. On 06/08/2016 09:55 AM, Francesca Strappini wrote: > I have only something similar in

Re: [Freesurfer] selxavg3-sess error

Hi Doug, it looks like my email with attached the Xtmp.mat file didn't arrive. How can I send it to you? Thanks! Francesca 2016-06-08 15:44 GMT+02:00 Douglas Greve : > Do you have both polar and eccen data? If so, can you send the Xtmp.mat > file? > > > On 6/8/16 6:08

Re: [Freesurfer] selxavg3-sess error

Do you have both polar and eccen data? If so, can you send the Xtmp.mat file? On 6/8/16 6:08 AM, Francesca Strappini wrote: Hi Freesurfer experts, I'm re-posting this message because I think it got lost. I'm trying to analyze some phase-encoded data with the eccentricity protocol for

[Freesurfer] selxavg3-sess error

Hi Freesurfer experts, I'm re-posting this message because I think it got lost. I'm trying to analyze some phase-encoded data with the eccentricity protocol for retinotopic data and I'm having troubles with selxavg3-sess. I run the following commands: mkanalysis-sess -analysis

[Freesurfer] selxavg3-sess error with phase-encoded data

Hi Freesurfer experts, I'm trying to analyze some phase-encoded data with the eccentricity protocol for retinotopic data and I'm having troubles with selxavg3-sess. I run the following commands: mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj lh -TR 2 -retinotopy 24 -paradigm

Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses

...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, June 01, 2016 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses Are you using selxavg-sess or selxavg3-sess

Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses

> 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: Wednesday, June 01, 2016 2:42 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: R

Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses

Wednesday, June 01, 2016 2:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses Don't include the -no-con-ok flag. For resting state, you don't need to run mkcontrast-sess because a contrast will automatically be created for you. On 06/

Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses

Don't include the -no-con-ok flag. For resting state, you don't need to run mkcontrast-sess because a contrast will automatically be created for you. On 06/01/2016 02:24 PM, Raney, Talia L. wrote: > Hi FreeSurfer users, > I have some resting state data that I preprocessed and conducted first

[Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses

Hi FreeSurfer users, I have some resting state data that I preprocessed and conducted first level analyses using the flag -no-con-ok. Since no ces.nii.gz or sig.nii.gz is createdcomes up because there is no contrast, I'm wondering if it's possible to conduct functional ROI analyses with the

Re: [Freesurfer] selxavg3-sess question

Yes, it is. I forgot that version 5.3 uses the brain mask from the first run. This is fixed in version 6. On 03/09/2016 02:42 PM, Ji Won Bang wrote: > Dear. Freesurfer experts. > > Hi. > > I'm pretty sure that this error is due to the different number of > slices in different runs > > I ran

Re: [Freesurfer] selxavg3-sess question

Dear. Freesurfer experts. Hi. I'm pretty sure that this error is due to the different number of slices in different runs I ran preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_Retino -nosmmth -per-run -force Then I ran selxavg3-sess -s $SUBJECT -analysis retino -df sessdirfile I thought

Re: [Freesurfer] selxavg3-sess problem: SVD input matrix contains NaN

It appears that you do not have any events for condition 3. Is that correct? Check your par files. doug On 02/08/2016 08:28 PM, Mcnorgan, Christopher wrote: > Hi Doug, > Thanks for looking at this. The .mat file is attached. Can you send me the Xtmp.mat file? On 2/2/16 6:40 PM,

Re: [Freesurfer] selxavg3-sess problem: SVD input matrix contains NaN

Can you send me the Xtmp.mat file? On 2/2/16 6:40 PM, Mcnorgan, Christopher wrote: > Hi, > I'm attempting an inaugural run through the FS pipeline on some event-related > data collected over 6 runs. I'm not sure if this makes any difference, but > the experiment is self-paced, and the events

[Freesurfer] selxavg3-sess problem: SVD input matrix contains NaN

Hi, I'm attempting an inaugural run through the FS pipeline on some event-related data collected over 6 runs. I'm not sure if this makes any difference, but the experiment is self-paced, and the events are of varying duration (it's a lexical decision task, and participants can take up to 4

Re: [Freesurfer] selxavg3-sess ERROR

hi doug, thank you so much for your quick reply. yes - I saw this error after I sent you the error log. I checked the paradigm file, corrected it and rerun everything. now this error is gone but I still get the following: Error using svd Input to SVD must not contain NaN or Inf. Error in cond

Re: [Freesurfer] selxavg3-sess ERROR

That means that your design matrix is ill-conditioned. This error means one of two things is wrong with your .par file (located in each run of each subject’s bold directory): 1) there are not two or more occurrences of one of your conditions; or 2) there is a pattern to your conditions (for

Re: [Freesurfer] selxavg3-sess ERROR

Did you see the error description: ERROR: /space/mdeh5/1/halgdev/projects/christina/FSFAST/Project/NC211_fmri_060515/Sess01/bold/004/oddeven.par is not correctly formatted. Line 19 only has 0 items did you check this file? On 12/09/2015 12:38 PM, Christina Pressl wrote: > Dear Freesurfer

Re: [Freesurfer] selxavg3-sess ERROR

I see, here is a copy of my paradigm 0. 2 11.100 0 21.100 3 32.200 0 42.200 2 53.300 0 63.300 2 74.400 0 84.400 1 95.500 0 105.500 1 116.600 0 126.600 3 137.700 0 147.700 3 158.800 0 168.800 1 179.900 0 I don’t see how this setup reflects one of the two potential errors you outlined.

[Freesurfer] selxavg3-sess ERROR

Dear Freesurfer Experts, I am having trouble with selxavg3-sess and was wondering if you could maybe help me resolving the issue (error log attached) I ran #preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run and the following commands for lh, rh and mni305

[Freesurfer] selxavg3-sess error empty conditions in paradigm file

Hello Freesurfer Experts, I am reposting this as this has not come up on the mail archive thread. I keep running into the following error (see below) when selxavg3-sess gets to my third subject. I am assuming this is because this subject does not have all of the conditions modeled (that is, this

Re: [Freesurfer] selxavg3-sess error empty conditions in paradigm file

There is not a way to model empty conditions. The easiest thing to do is to just change another condition to say it is the missing condition. It should have little effect on the final results. On 11/18/2015 02:06 PM, Danielle Miller wrote: > Hello Freesurfer Experts, > > I am reposting this as

[Freesurfer] selxavg3-sess error

Hello Freesurfer Experts, I keep running into the following error (see below) when selxavg3-sess gets to my third subject. I am assuming this is because this subject does not have all of the conditions modeled (that is, this particular subject does not have any incorrect responses). Is there a

Re: [Freesurfer] selxavg3-sess outputs

Yes, they do. There is also a pcc.nii.gz which is the partial correlation coefficient. On 9/30/15 1:14 PM, Jiahe Zhang wrote: Dear Freesurfer experts, The freesurfer command 'selxavg3-sess' outputs many files in the contrast folder in addition to the three documented on the Wiki (ces,

[Freesurfer] selxavg3-sess outputs

Dear Freesurfer experts, The freesurfer command 'selxavg3-sess' outputs many files in the contrast folder in addition to the three documented on the Wiki (ces, cesvar, sig). Is there more detailed documentation on what each output is and how they're computed? In particular, I was wondering if the

Re: [Freesurfer] selxavg3-sess error

...@mgh.harvard.edu] Sent: Thursday, July 30, 2015 6:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] selxavg3-sess error Hi Doug, Attached is doug2.log. Thanks, Anais From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun

Re: [Freesurfer] selxavg3-sess error

[gr...@nmr.mgh.harvard.edu] Sent: Friday, August 21, 2015 1:46 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error I thought this problem was fixed when you eliminated the multiple formats (?) On 8/20/15 12:03 PM, Rodriguez-Thompson, Anais wrote: Hi Doug, I sent

[Freesurfer] selxavg3-sess error

: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rodriguez-Thompson, Anais [arodriguez-thomp...@mgh.harvard.edu] Sent: Thursday, July 30, 2015 6:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] selxavg3-sess error Hi Doug, Attached is doug2.log

Re: [Freesurfer] selxavg3-sess, -svres

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess, -svres They are not the same. As you point out they have a correlation of .98, not 1.0. What you are discovering is the inconvenient truth that task signal accounts for a very small proportion of variation

Re: [Freesurfer] selxavg3-sess, -svres

They are not the same. As you point out they have a correlation of .98, not 1.0. What you are discovering is the inconvenient truth that task signal accounts for a very small proportion of variation. Welcome to fMRI:). I think the reason why the residual does not equal y - X*beta is that they

[Freesurfer] selxavg3-sess, -svres

Hi Doug, In order to understand my data better, I did the following analysis. First, I did a full model analysis with all stimuli conditions included in the analysis using: mkanalysis-sess -fsd bold -paradigm xy_mky_category_eye_weights.par -event-related -refeventdur 1 -no-inorm -delay 0

[Freesurfer] selxavg3-sess error

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error ok, still not sure what is happening. Can you try preproc-sess -debug -s GDDA001 -d /autofs/cluster/roffman/users/Stable5_PerRun -a SIRP_LoadRegression_Stable5_072915 | tee doug2.log and send me doug2.log On 07/30/2015 12:54 PM

Re: [Freesurfer] selxavg3-sess error

:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] selxavg3-sess error Hi Doug, Attached is doug2.log. Thanks, Anais From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr

Re: [Freesurfer] selxavg3-sess error

...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, July 30, 2015 12:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error those look ok. Can you run your selxavg3-sess command

Re: [Freesurfer] selxavg3-sess error

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error ok, still not sure what is happening. Can you try preproc-sess -debug -s GDDA001 -d /autofs/cluster/roffman/users/Stable5_PerRun -a SIRP_LoadRegression_Stable5_072915 | tee doug2.log and send me doug2.log On 07/30/2015 12:54 PM, Rodriguez

[Freesurfer] selxavg3-sess error

Hi Freesurfer experts, I'm having trouble running selxavg3-sess in 5.3 because it is looking for a file that does not exist (fmcpr.sm5.nii.gz). I read in another freesurfer mail thread that this issue can be fixed by preprocessing the subject. However, even after re-preprocessing my subjects

Re: [Freesurfer] selxavg3-sess error

, 2015 12:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error What is your preproc-sess command and your mkanalysis-sess command? On 07/30/2015 12:00 PM, Rodriguez-Thompson, Anais wrote: Hi Freesurfer experts, I'm having trouble running selxavg3-sess in 5.3

Re: [Freesurfer] selxavg3-sess error

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error those look ok. Can you run your selxavg3-sess command with -debug and capture the output in a log file? Eg, selxavg3-sess -s sess -a SIRP_LoadRegression_Stable5_072915 -debug | tee doug.log and send me doug.log On 07/30/2015 12:09 PM, Rodriguez

Re: [Freesurfer] selxavg3-sess error

, July 30, 2015 12:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error What is your preproc-sess command and your mkanalysis-sess command? On 07/30/2015 12:00 PM, Rodriguez-Thompson, Anais wrote: Hi Freesurfer experts, I'm having trouble running selxavg3-sess

Re: [Freesurfer] selxavg3-sess error

What is your preproc-sess command and your mkanalysis-sess command? On 07/30/2015 12:00 PM, Rodriguez-Thompson, Anais wrote: Hi Freesurfer experts, I'm having trouble running selxavg3-sess in 5.3 because it is looking for a file that does not exist (fmcpr.sm5.nii.gz). I read in another

Re: [Freesurfer] selxavg3-sess CPU limits

thanks! in your experience, is there a big performance deficit when using -singleCompThread? caspar 2015-05-28 14:57 GMT-04:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: This is actually a matlab problem. In the next version I have fixed this so that it only uses one cpu. You can't control the

Re: [Freesurfer] selxavg3-sess CPU limits

I don't know. I mainly got annoyed that my desktop would freeze up when doing fmri analysis. On 05/28/2015 03:15 PM, Caspar M. Schwiedrzik wrote: thanks! in your experience, is there a big performance deficit when using -singleCompThread? caspar 2015-05-28 14:57 GMT-04:00 Douglas N Greve

Re: [Freesurfer] selxavg3-sess svd NaN error

can you send /autofs/cluster/neuromind/dwakeman/mm/subjects/nmr00904/sycabs/sycabs_lh/pr014/Xtmp.mat ? On 03/26/2015 03:51 PM, dgw wrote: Hi, I am having a problem running my selxavg3-sess using Freesurfer 5.3.0 stable. I am getting the following error: Saving X matrix to

Re: [Freesurfer] selxavg3-sess svd NaN error

The duration of the stimuli for condition 4 is only 8 milisec. What's up with that? If this is what you want, then go into the analysis.info file and change the TER to something like .007974 (your TR/153). You'll have to do this for all your analyses. The TER is the basic clock tick of the

Re: [Freesurfer] selxavg3-sess svd NaN error

Actually, I just noticed that I had a flag in mkanalysis-sess that does this. It is -TER doug On 03/26/2015 08:15 PM, Douglas N Greve wrote: The duration of the stimuli for condition 4 is only 8 milisec. What's up with that? If this is what you want, then go into the analysis.info file and

[Freesurfer] selxavg3-sess svd NaN error

Hi, I am having a problem running my selxavg3-sess using Freesurfer 5.3.0 stable. I am getting the following error: Saving X matrix to /autofs/cluster/neuromind/dwakeman/mm/subjects/nmr00904/sycabs/sycabs_lh/pr014/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond

[Freesurfer] selxavg3-sess error

Dear FS experts, I got an error while running selxavg3-sess for a single subject. The log (attached) says the following: * ** Input 018/tmp.mc-afni2.7515/invol.nii.gz and base 018/tmp.mc-afni2.7515/tempvol.nii.gz don't have same

Re: [Freesurfer] selxavg3-sess error

...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] *Sent:* Monday, March 09, 2015 2:49 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] selxavg3-sess error What is your mris_preproc command? And your mkanalysis-sess

Re: [Freesurfer] selxavg3-sess error

, March 09, 2015 2:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error It looks like different runs have different number of slices. Is that right? On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote: Dear FS experts, I got an error while running selxavg3-sess

Re: [Freesurfer] selxavg3-sess error

*From:* freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] *Sent:* Monday, March 09, 2015 2:38 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] selxavg3-sess error It looks like different

Re: [Freesurfer] selxavg3-sess error

It looks like different runs have different number of slices. Is that right? On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote: Dear FS experts, I got an error while running selxavg3-sess for a single subject. The log (attached) says the following:

Re: [Freesurfer] selxavg3-sess error

Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, March 09, 2015 2:49 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error What is your mris_preproc command? And your mkanalysis-sess command? On 3/9/15 2:41 PM, Eryilmaz, H. Hamdi wrote: Hi Doug, Yes, that's correct

Re: [Freesurfer] selxavg3-sess

You need to have matlab in your path to run selxavg3-sess (octave should work as well) On 01/10/2015 07:08 PM, std...@virgilio.it wrote: Hi list, the selxavg3-sess -s Sess01 -a fc.lpccseed.surf.lh in fcMRI analysis produces this error. rawfunc2surf-sess completed

[Freesurfer] selxavg3-sess

Hi list, the selxavg3-sess -s Sess01 -a fc.lpccseed.surf.lh in fcMRI analysis produces this error. rawfunc2surf-sess completed Started at Sun Jan 11 00:50:53 CET 2015 Ended at Sun Jan 11 00:50:54 CET 2015 preproc-sess done

Re: [Freesurfer] selxavg3-sess error

It is not looking for fmc.sm5.DM.lh.nii.gz but rather fmcsm5.nii.gz in /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001 does that file exist? Have you run preproc-sess? doug On 8/28/14 9:49 AM, Francesca Strappini wrote: Dear all, I've run selxavg3-sess and I got this error

Re: [Freesurfer] selxavg3-sess error

Thank you, now it works! Best Francesca 2014-09-08 15:24 GMT+03:00 Douglas Greve gr...@nmr.mgh.harvard.edu: It is not looking for fmc.sm5.DM.lh.nii.gz but rather fmcsm5.nii.gz in /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001 does that file exist? Have you run preproc-sess?

[Freesurfer] selxavg3-sess error

Dear all, I've run selxavg3-sess and I got this error message when it tried to read the fmcsm file (fmc.sm5.DM.lh.nii.gz). Thank you for your help, Francesca shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy selxavg3-sess -a rtopy.DM.lh -s SUBJ01 Surface data DM lh

  1   2   >