[Freesurfer] Running Several Versions of fsfast GLM In Parallel Leads to "Stale File Handles"
Hello, I have been trying to run several versions of the same GLM analysis, trying out different parameters to see if they affect the results. For instance, I am running the GLM with different levels of smoothing, per-session versus per-run motion correction, etc. To speed this up, I am trying to do these GLMs in parallel. However, when I do this, I run into a "stale file handle" problem. As near as I can tell, this occurs because the analyses try to read and write to the same log files at the same time. A typical error message is "/net/rcss2/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/fpoinfips01/scripts/glm/log/preproc-160718_xu_loc01_sub02-bold.log: Stale file handle". I have tried putting "-nolog" in the call to selxavg3-sess, but this doesn't prevent the creation of log files when it makes the sub-calls to the various pre-processing functions. Is there any way around this? It would be rather slow to try to run the GLMs sequentially, so I am wondering if anybody has figured out a way around this problem. Much obliged, JohnMark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Running Retinotopy in FSFAST, Design Matrix has Empty Regressors
Hello, I am trying to run a retinotopy analysis in fsfast, using only polar angle. However, when I try to run it, I am getting the error "Input to SVD must not contain NaN or Inf." I have traced this error and it looks like the design matrix X has 12 regressors (the first 12) that consist solely of zeros. I am using the following commands: mkanalysis-sess -analysis retinotopy -fsd bold -runlistfile runlist.txt -native -funcstem fmc -nuisreg mcextreg 3 -retinotopy 36.4 -per-session -paradigm retino.par -inorm -spmhrf 0 -TR .650 -polyfit 2 -nskip 19 selxavg3-sess -analysis retinotopy -sf sublist.txt -df sessdir Any idea what the first 12 regressors in the design matrix might correspond to in retinotopy analyses and why they'd be empty? I have looked at the documentation and there doesn't seem to be a clear labeling of the retinotopy design matrix anywhere, although perhaps I'm missing something. Thank you very much, JohnMark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Can't Load More Than Four Unique Overlays on TKSurfer From Command Line
Hello, I am trying to load five overlays on TKSurfer from the command line (actual command attached). The problem is this: if I try to load five different overlays, the fifth one will show up on Freesurfer as being identical to the first one (for instance, in this example, the "all-slope" overlay will appear visually identical to the "fs-slope" overlay, even though I've verified that the files are different). Furthermore, if you try to load six, then the fifth overlay will look the same as the first, the sixth will look the same as the second, and so forth. If I manually add the overlays from the menu in tksurfer this doesn't happen, but I'd prefer not to have to do this. Any idea what could be going on? Apologies that the command is a mess to read: in case it isn't clear, I am calling the overlay flag five separate times, once for each desired overlay. Thanks, JohnMark tksurfer green_ant lh inflated -gray -title green_ant_lh *-overlay* /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/glm_sm5_ps/fs-slope/sig.nii.gz -orf /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/register.dof6.dat -fminmax 2 5 *-overlay* /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/glm_sm5_ps/fo-slope/sig.nii.gz -orf /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/register.dof6.dat -fminmax 2 5 *-overlay* /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/glm_sm5_ps/ps-slope/sig.nii.gz -orf /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/register.dof6.dat -fminmax 2 5 *-overlay* /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/glm_sm5_ps/po-slope/sig.nii.gz -orf /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/register.dof6.dat -fminmax 2 5 *-overlay* /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/glm_sm5_ps/all-slope/sig.nii.gz -orf /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/register.dof6.dat -fminmax 2 5 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Viewing Retinotopy In Freeview
Hello, I am thinking of switching from Tksurfer to Freeview, but I want to make sure that retinotopy visualization still works well. Is it straightforward to view phase-encoded displays? There are a few options on tksurfer (complex color wheel, ability to set number of cycles and angle offset for phase encoded display, ability to smooth overlay) that I am not able to immediately find on freeview. Currently, to visualize retinotopy data we are using the strategy of loading both the real and complex parts of the display on tksurfer. Are there analogous ways of doing all these steps on freeview as of yet, or are they still waiting to be implemented? Thank you very much, JohnMark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Best way to run GLM on a single subject across multiple sessions?
Hello, I am looking to run a GLM on a single subject, where data was collected across several different sessions. What is the best way to go about doing this in the FSFAST pipeline? I was thinking that I should just 1) drop the data for all the runs into a single BOLD directory as though they were from a single session, and 2) let the registration and motion correction do as well as they can. Is this a reasonable approach, and if so, are there any settings in the preprocessing or GLM that would advisable (for instance, in terms of running the GLM on the surface versus the volume, or doing the registration per-run versus per-session)? Thank you very much, JohnMark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 when doing analyses in native volume space, so I am not
sure why selxavg-sess is looking for the wrong file path. For reference,
here is my call to mkanalysis-sess:
mkanalysis-sess -analysis analysis_name -fsd bold -runlistfile runlist.txt
-native -nuisreg mcextreg 3 -fwhm 0 -event-related -nconditions 8
-paradigm spiralpara.par -spmhrf 0 -refeventdur 12 -TR 1.5
-polyfit 2 -nskip 8
I am using Freesurfer 5.3, if that helps. The analysis works fine when I
apply 3mm smoothing (I've done preprocessing for both the 0mm and 3mm
options).
Thank you very much, and cheers,
JohnMark
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[Freesurfer] Difference in Recon-All Output Between Freesurfer Versions?
Hello, Recently, I re-ran recon-all with Freesurfer version 5 on some subjects whose surfaces had previously been reconstructed with Freesurfer version 4. As a result, it appears that their surface reconstructions have subtly changed, such that the labels that were specified in the old reconstruction are all messed up in the new reconstruction (since the surfaces that they were once associated with have changed). Did recon-all change between Freesurfer versions, and if so, is there a way to go back to the old algorithm short of simply switching back to Freesurfer version 4? It is possible that I have accidentally changed something else and that's why the surface files are different, but I wanted to see if there were any changes in the reconstruction algorithm between versions that might have caused this. Thank you very much, JohnMark Taylor ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Difference in Recon-All Output Between Freesurfer Versions?
(the reason I did this was because the new Freesurfer version outputs labels for perirhinal cortex as part of the reconstruction process, and we were interested in using this ROI in our analyses; as an additional question, is there a way of producing these anatomical labels without reconstructing the surface from scratch?) On Mon, Apr 10, 2017 at 5:46 PM, Taylor, Johnmark < johnmarktay...@g.harvard.edu> wrote: > Hello, > > Recently, I re-ran recon-all with Freesurfer version 5 on some subjects > whose surfaces had previously been reconstructed with Freesurfer version 4. > As a result, it appears that their surface reconstructions have subtly > changed, such that the labels that were specified in the old reconstruction > are all messed up in the new reconstruction (since the surfaces that they > were once associated with have changed). Did recon-all change between > Freesurfer versions, and if so, is there a way to go back to the old > algorithm short of simply switching back to Freesurfer version 4? It is > possible that I have accidentally changed something else and that's why the > surface files are different, but I wanted to see if there were any changes > in the reconstruction algorithm between versions that might have caused > this. > > Thank you very much, > > JohnMark Taylor > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FSFAST Full Model Residuals?
Hello, I had a quick question. Is there a way to make FSFAST output a 4D volume of all the residuals? In other words: is there a way to see, for each voxel and timepoint, how much of the BOLD response was unexplained by the GLM? I know that it outputs a volume containing the residual variances, but I am interested in looking at the residuals in more detail. I see that there is a directory called "res", but for all of the GLMs I've run it appears to be empty... Thank you very much, JohnMark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FSFAST Full Model Residuals?
Actually, just noticed that this is an option in selxavg3-sess, never mind! On Wed, Jun 7, 2017 at 9:07 PM, Taylor, Johnmark < johnmarktay...@g.harvard.edu> wrote: > Hello, > > I had a quick question. Is there a way to make FSFAST output a 4D volume > of all the residuals? In other words: is there a way to see, for each voxel > and timepoint, how much of the BOLD response was unexplained by the GLM? I > know that it outputs a volume containing the residual variances, but I am > interested in looking at the residuals in more detail. I see that there is > a directory called "res", but for all of the GLMs I've run it appears to be > empty... > > Thank you very much, > > JohnMark > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Retrieving Model R^2 From FSFAST GLM Output?
Hello, Is there a simple way to retrieve the R^2 of the GLM model fit for each voxel from the output of FSFAST? I wonder if rho1.nii.gz might be relevant, but I couldn't find any documentation on this particular file. Thank you very much, JohnMark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Strange Discrepancy Between Activation Location on Surface vs. Volume
Hello, I am running into an odd issue. In particular, I have run a GLM analysis in *volume* space, and I am visualizing the results both on the surface using tksurfer, and on the volume using tkmedit. In both cases, I am using the register.dof6.dat file to do the registration. Oddly, when I visualize the results on the *surface*, the activation patch falls on the medial surface of the hemisphere, in the *precuneus*, whereas when I visualize the results on the *volume*, the patch is in the *intraparietal sulcus* (which is where we expect to see this particular activation). I have made a label out of the activation in both cases and viewed it in the other space just to make sure that it is in fact the same activation, and it is. Any idea what might be going on? It seems to me that it can't be an issue with the BOLD volume --> structural volume registration, since the activations look normal on tkmedit. It seems to me, then, that it must have to do with the relationship between the anatomical volume and the anatomical surface--could this be where the problem lies? Maybe an imperfect surface reconstruction? Thank you very much, JohnMark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Combining Results of Per-Run GLM?
Hello, I am trying to do a GLM analysis for a study in which I scanned each participant twice. Currently, to combine the two scanning sessions I am combining the runs from the two sessions into a single session directory and applying per-session motion correction, essentially treating all the data as though it came from a single session. The issue is that when I do this, the GLM analysis takes prohibitively long (with just 8 subjects, the analysis has already been running for two weeks). To speed things up, I had the idea of doing the runwise GLM (getting the betas and contrast values for each run), then combining the runwise results to get t-values and p-values for the whole session. However, I am not entirely sure how to do this last bit; is there some kind of function that can be used to take all the per-run t-values or effect sizes in a session and combine them to get an aggregate t-value and p-value for the whole session, for a given contrast? I believe FSL follows this analysis strategy (doing runwise analyses then combining them into the whole session), so I was wondering whether FSFAST had a way of doing the same. Thank you very much, JohnMark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fixed Effects Analysis on Single Subject's Brain
Hello, Quick question. If I scanned a single subject across several sessions and want to do a fixed effects analysis on that subject's brain (without registering to MNI or Talairach space), how do I go about doing this? I am trying to us isxconcat-sess and then mri_glmfit, but I am not seeing an option to simply do the analysis in native space instead of registering to a standard brain. Is there a way to do this besides taking the end result of the analysis and doing the reverse registration back to the subject's brain? JohnMark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess
Hello, A few quick questions about the "Per-Run" option in preproc-sess. I understand that in this option, each run's images are registered to the middle timepoint of that run, rather than the first timepoint of the first run. I was wondering, though: 1) Why is this the preferred option instead of per-session? 2) If motion-correction is only done internally to each run, then wouldn't between-run motion throw things off if you wanted to do a GLM spanning the whole scanning session (although I assume it'd be fine for single-run GLMs)? What ensures that the images line up properly between runs? Thank you very much, JohnMark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess
Thank you, this is very helpful! A few quick followup questions: 1) If you don't specifically tell preproc-sess what space to resample too (e.g., by using the "-surface" or "-mni305" flags), does it automatically resample to the subject's anatomical volume, then? 2) If fmc.nii.gz is already registered to the subject's volume, then how come a registration file has to be specified when visualizing GLM results using tksurfer? If fmc.nii.gz is already resampled to anatomical space, then surely any GLM contrasts should be as well, no? 3) If per-run motion correction and registration is specified in pre-proc sess, then there will be a different functional-->structural transformation for each run, correct? If this is the case, then when visualizing session-wide GLM results using tksurfer, which registration file should be specified when loading up the overlay, since there'll be a different registration file for each run? Apologies for these (probably basic) questions, I just want to make sure I am crystal-clear on what preproc-sess is doing. Cheers, and many thanks, JohnMark On Mon, Dec 4, 2017 at 3:20 PM, wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > >1. Re: mri_binarize (Douglas N Greve) >2. Re: Clarification about "Per-Run" Motion Correction and > Registration in Preproc-Sess (Douglas N Greve) >3. Re: freesurfer design (Douglas N Greve) >4. Re: subcortical structures volume (Douglas N Greve) >5. Re: mri_vol2surf wrong hemisphere (Douglas N Greve) >6. Re: Concatenating .mgh surface space functional MRI runs > (Douglas N Greve) >7. Re: QDEC and comparing two conditions (Douglas N Greve) >8. Re: Combining parcellated regions within an atlas? > (Douglas N Greve) >9. Re: Overlaying multiple results onto one surface (Douglas N Greve) > 10. recon edit error (Nicole Orme) > > > -- > > Message: 1 > Date: Mon, 4 Dec 2017 12:30:33 -0500 > From: Douglas N Greve > Subject: Re: [Freesurfer] mri_binarize > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <9d91f7ea-a55b-cd78-2b55-687cf2078...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > you can do it in two steps. First, use mri_binarize to create a mask of > the structutures you want. Then use mri_mask to apply the mask to the > aparc.DKT file > > > On 12/03/2017 07:44 AM, John Anderson wrote: > > Dear FS experts, > > I want to use mri_binarize to create (binarized and free of CSF and > > ventricles) mask from "aparc.DKTatlas+aseg". How can I substract CSF > > and ventricles from teh atlas using mri_binarize? > > > > Thanks > > John > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- > > Message: 2 > Date: Mon, 4 Dec 2017 12:32:00 -0500 > From: Douglas N Greve > Subject: Re: [Freesurfer] Clarification about "Per-Run" Motion > Correction and Registration in Preproc-Sess > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <813a5a08-d27e-a2a6-8472-66f998aaa...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 12/03/2017 06:35 PM, Taylor, Johnmark wrote: > > Hello, > > > > A few quick questions about the "Per-Run" option in preproc-sess. I > > understand that in this option, each run's images are registered to > > the middle timepoint of that run, rather than the first timepoint of > > the first run. I was wondering, though: > > >
[Freesurfer] Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess
Thanks once again for all the help on this. I am running the GLM in native space, typically so that I can get the beta values to use in an MVPA analysis. So it sounds like if you specify per-run motion-correction and registration, and don't tell it to resample to anything (e.g., the MNI brain or the surface), then there's no guarantee that the voxels will properly line up if you want to do, for instance, a single-subject GLM in the subject's native space? So in this case, per-session motion correction would be better so that all the functional volumes in the session are registered properly? > Thank you, this is very helpful! A few quick followup questions: > > 1) If you don't specifically tell preproc-sess what space to resample > too (e.g., by using the "-surface" or "-mni305" flags), does it > automatically resample to the subject's anatomical volume, then? I don't think it will do anything if you don't specify > > 2) If fmc.nii.gz is already registered to the subject's volume, then > how come a registration file has to be specified when visualizing GLM > results using tksurfer? If fmc.nii.gz is already resampled to > anatomical space, then surely any GLM contrasts should be as well, no? fmc is not registered to the anatomical, it is registered to the template. The template is registered to the anat through the registration file. The data are still in the native functional space. > > 3) If per-run motion correction and registration is specified in > pre-proc sess, then there will be a different functional-->structural > transformation for each run, correct? Correct > If this is the case, then when visualizing session-wide GLM results > using tksurfer, which registration file should be specified when > loading up the overlay, since there'll be a different registration > file for each run? In what space are you doing the GLM? Usually, the raw data are resampled onto the surface (eg, fmc.fsaverage.lh.sm05.nii.gz), and the GLM is done in this spae.so no registration is needed. > > Apologies for these (probably basic) questions, I just want to make > sure I am crystal-clear on what preproc-sess is doing. > > Cheers, and many thanks, > > JohnMark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Global Signal Scaling in FSFAST Pipeline
Hello, When using preproc-sess and selxavg3-sess, how is global mean scaling handled? Is the session-wide (4D) mean subtracted, is each volume's mean subtracted, or neither? Thank you very much, JohnMark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Global Signal Scaling in FSFAST Pipeline
Never mind, found the answer online, sorry about that! On Mon, Dec 11, 2017 at 2:13 PM, Taylor, Johnmark < johnmarktay...@g.harvard.edu> wrote: > Hello, > > When using preproc-sess and selxavg3-sess, how is global mean scaling > handled? Is the session-wide (4D) mean subtracted, is each volume's mean > subtracted, or neither? > > Thank you very much, > > JohnMark > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
