Re: [Freesurfer] Mri_mask producing only zeros
External Email - Use Caution Here is how I made the label into a surface overlay: mri_label2vol --label $label/lh.7Networks_6.label --temp /data/project/vislab/a/HCP_diff_Sara/fsaverage/mri/orig.mgz --identity --o $vols/lh.7Networks_6.nii mri_vol2surf --src $vols/lh.7Networks_6.nii --out $surfs/lh.7Networks_6.mgh --regheader fsaverage --hemi lh Here is the mri_mask command: mri_mask betamaskedFPcflh.mgh $surfs/lh.7Networks_6.mgh betasigandlabelmaskedFPcflh.mgh Output from mri_mask: DoAbs = 0 INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to betasigandlabelmaskedFPcflh.mgh...done. Sara A. Sims, MA Medical/Clinical Psychology Program UAB | The University of Alabama at Birmingham CIRC Suite 252A | 1719 6th Avenue South | Birmingham, AL 35294 P: 205.975.4060 | sno...@uab.edu On 10/14/19, 2:35 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: Hi Sara we will need to know the actual commands and the screen output from them that you ran cheers Bruce On Mon, 14 Oct 2019, Sims, Sara A (Campus) wrote: > > External Email - Use Caution > > Freesurfers, > > I am trying to use mri_mask using surface overlays. I made a label into a > volume and then into a surface with 1s inside the label and 0s outside the > label. I want to make a connectivity map surface overlay with values only > within my label overlay. However when I run it, it creates a surface overlay > with only zeros. There is definitely values within the label surface overlay > (I triple checked). > > Code I used: > > Mri_mask original_surface_overlay label_mask new_masked_output > > > > It doesn’t output any errors. > > Here is what it looks like in freeview: > > Original surface overlay (label is outlined in green) > > [IMAGE] > > The label made into a surface overlay (same as the one shown in green > above): > > [IMAGE] > > But this is the output: all zeros even though there was data within the > mask. > > [IMAGE] > > > > Help! > > Sara A. Sims > > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Mri_mask producing only zeros
External Email - Use Caution Freesurfers, I am trying to use mri_mask using surface overlays. I made a label into a volume and then into a surface with 1s inside the label and 0s outside the label. I want to make a connectivity map surface overlay with values only within my label overlay. However when I run it, it creates a surface overlay with only zeros. There is definitely values within the label surface overlay (I triple checked). Code I used: Mri_mask original_surface_overlay label_mask new_masked_output It doesn’t output any errors. Sara A. Sims ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Extracting mean of values within a lable
External Email - Use Caution Oh, I thought mri_segstats only took volumes. Can I feed it a surface with this flag: --surf-ctx-vol? Sara Sims From: on behalf of "Greve, Douglas N.,Ph.D." Reply-To: Freesurfer support list Date: Saturday, April 20, 2019 at 12:07 PM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Extracting mean of values within a lable look at mri_segstats. Run it with --help to get examples. Note that if your input volume has multiple frames, you can use --avgwf to get means of all the frames On 4/19/2019 4:46 PM, Sims, Sara A (Campus) wrote: External Email - Use Caution Hello! I have a surface overlay that I want to extract the mean of the values within a label and export to a text file. How can I do that? I was looking into mris_anatomical_stats, but does mris_anatomical_stats let you tell it what file to pull the data from instead of just doing the standard extractions? Alternatively, I would be fine with just extracting all the values within the label and then finding the mean on my own. How could I extract all the values within the label and exporting to a text file? Thanks, Sara Sims ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Extracting mean of values within a lable
External Email - Use Caution Hello! I have a surface overlay that I want to extract the mean of the values within a label and export to a text file. How can I do that? I was looking into mris_anatomical_stats, but does mris_anatomical_stats let you tell it what file to pull the data from instead of just doing the standard extractions? Alternatively, I would be fine with just extracting all the values within the label and then finding the mean on my own. How could I extract all the values within the label and exporting to a text file? Thanks, Sara Sims ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_preproc not running
External Email - Use Caution Here is the output file with debug on: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=bes7rp27gk0 Thanks, Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 sno...@uab.edu On 4/2/19, 3:34 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D." wrote: Can you run it with --debug as the first option, capture the terminal output, and send it to me? On 4/2/19 4:02 PM, Sims, Sara A (Campus) wrote: > > External Email - Use Caution > > My reply was not posted, most likely because the email is too large so > here is the script: > > mris_preproc --target fsaverage --hemi lh --no-prune --isp > $in/DMN/100206.newfar/lhsurf.mgh --isp > $in/DMN/100206.newcentral/lhsurf.mgh --isp > $in/DMN/100307.newfar/lhsurf.mgh --isp > $in/DMN/100307.newcentral/lhsurf.mgh --isp > $in/DMN/100408.newfar/lhsurf.mgh --isp > $in/DMN/100408.newcentral/lhsurf.mgh --isp > $in/DMN/100610.newfar/lhsurf.mgh --isp > $in/DMN/100610.newcentral/lhsurf.mgh --isp > $in/DMN/101006.newfar/lhsurf.mgh --isp > $in/DMN/101006.newcentral/lhsurf.mgh --isp > $in/DMN/101107.newfar/lhsurf.mgh --isp > $in/DMN/101107.newcentral/lhsurf.mgh --isp > $in/DMN/101309.newfar/lhsurf.mgh --isp > $in/DMN/101309.newcentral/lhsurf.mgh --isp > $in/DMN/101410.newfar/lhsurf.mgh --isp > $in/DMN/101410.newcentral/lhsurf.mgh --isp > $in/DMN/101915.newfar/lhsurf.mgh --isp > $in/DMN/101915.newcentral/lhsurf.mgh --isp > $in/DMN/102008.newfar/lhsurf.mgh --isp > $in/DMN/102008.newcentral/lhsurf.mgh --isp > $in/DMN/102311.newfar/lhsurf.mgh --isp > $in/DMN/102311.newcentral/lhsurf.mgh --isp > $in/DMN/102513.newfar/lhsurf.mgh --isp > $in/DMN/102513.newcentral/lhsurf.mgh --isp > $in/DMN/102816.newfar/lhsurf.mgh --isp > $in/DMN/102816.newcentral/lhsurf.mgh --isp > $in/DMN/103111.newfar/lhsurf.mgh --isp > $in/DMN/103111.newcentral/lhsurf.mgh --isp > $in/DMN/103414.newfar/lhsurf.mgh --isp > $in/DMN/103414.newcentral/lhsurf.mgh --isp > $in/DMN/103515.newfar/lhsurf.mgh --isp $in/DMN/103515.n > > ….. --out $out/preproc_DMN_fc/lh.paired-diff.DMN_fc.mgh --f $sublist > --no-cortex-only > > I also double checked with our research computing department to make > sure I was referencing the command you sent me previously. > > Sara Sims > > Graduate Research Fellow > > University of Alabama at Birmingham > > Department of Psychology > > 205-975-4060 > > sno...@uab.edu > > *From: * on behalf of "Greve, > Douglas N.,Ph.D." > *Reply-To: *Freesurfer support list > *Date: *Saturday, March 30, 2019 at 6:06 PM > *To: *"freesurfer@nmr.mgh.harvard.edu" > *Subject: *Re: [Freesurfer] mris_preproc not running > > Hi Sara, can you just cut and paste them into the email. And are you > sure you're running the new command? > > On 3/29/19 6:59 PM, Sims, Sara A (Campus) wrote: > > External Email - Use Caution > > I have attached them here. > > Sara Sims > > Graduate Research Fellow > > University of Alabama at Birmingham > > Department of Psychology > > 205-975-4060 > > sno...@uab.edu <mailto:sno...@uab.edu> > > On 3/29/19, 10:05 AM,"freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, > Douglas N.,Ph.D." <mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D.> dgr...@mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofdgr...@mgh.harvard.edu> wrote: > > Can you send your full command line and the full terminal output? Are > > you sure you're using the new command? > > > > On 3/27/19 10:33 PM, Sims, Sara A (Campus) wrote: > > > External Email - Use Caution > > > > > > Doug, > > > I have implemented the new version of the command. I am getting this error when I add the no-prune flag to my script. > > > ERROR: could not find volume --no-prune. Does it exist? > > > ERROR: reading --no-prune > > > Are there specifics with where in the comma
Re: [Freesurfer] mris_preproc not running
External Email - Use Caution My reply was not posted, most likely because the email is too large so here is the script: mris_preproc --target fsaverage --hemi lh --no-prune --isp $in/DMN/100206.newfar/lhsurf.mgh --isp $in/DMN/100206.newcentral/lhsurf.mgh --isp $in/DMN/100307.newfar/lhsurf.mgh --isp $in/DMN/100307.newcentral/lhsurf.mgh --isp $in/DMN/100408.newfar/lhsurf.mgh --isp $in/DMN/100408.newcentral/lhsurf.mgh --isp $in/DMN/100610.newfar/lhsurf.mgh --isp $in/DMN/100610.newcentral/lhsurf.mgh --isp $in/DMN/101006.newfar/lhsurf.mgh --isp $in/DMN/101006.newcentral/lhsurf.mgh --isp $in/DMN/101107.newfar/lhsurf.mgh --isp $in/DMN/101107.newcentral/lhsurf.mgh --isp $in/DMN/101309.newfar/lhsurf.mgh --isp $in/DMN/101309.newcentral/lhsurf.mgh --isp $in/DMN/101410.newfar/lhsurf.mgh --isp $in/DMN/101410.newcentral/lhsurf.mgh --isp $in/DMN/101915.newfar/lhsurf.mgh --isp $in/DMN/101915.newcentral/lhsurf.mgh --isp $in/DMN/102008.newfar/lhsurf.mgh --isp $in/DMN/102008.newcentral/lhsurf.mgh --isp $in/DMN/102311.newfar/lhsurf.mgh --isp $in/DMN/102311.newcentral/lhsurf.mgh --isp $in/DMN/102513.newfar/lhsurf.mgh --isp $in/DMN/102513.newcentral/lhsurf.mgh --isp $in/DMN/102816.newfar/lhsurf.mgh --isp $in/DMN/102816.newcentral/lhsurf.mgh --isp $in/DMN/103111.newfar/lhsurf.mgh --isp $in/DMN/103111.newcentral/lhsurf.mgh --isp $in/DMN/103414.newfar/lhsurf.mgh --isp $in/DMN/103414.newcentral/lhsurf.mgh --isp $in/DMN/103515.newfar/lhsurf.mgh --isp $in/DMN/103515.n ….. --out $out/preproc_DMN_fc/lh.paired-diff.DMN_fc.mgh --f $sublist --no-cortex-only I also double checked with our research computing department to make sure I was referencing the command you sent me previously. Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 sno...@uab.edu From: on behalf of "Greve, Douglas N.,Ph.D." Reply-To: Freesurfer support list Date: Saturday, March 30, 2019 at 6:06 PM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] mris_preproc not running Hi Sara, can you just cut and paste them into the email. And are you sure you're running the new command? On 3/29/19 6:59 PM, Sims, Sara A (Campus) wrote: External Email - Use Caution I have attached them here. Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 sno...@uab.edu<mailto:sno...@uab.edu> On 3/29/19, 10:05 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D."<mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D.> <mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofdgr...@mgh.harvard.edu> wrote: Can you send your full command line and the full terminal output? Are you sure you're using the new command? On 3/27/19 10:33 PM, Sims, Sara A (Campus) wrote: > External Email - Use Caution > > Doug, > I have implemented the new version of the command. I am getting this error when I add the no-prune flag to my script. > ERROR: could not find volume --no-prune. Does it exist? > ERROR: reading --no-prune > Are there specifics with where in the command line it should go? I have tried it near the beginning and near the end and still get this error. > > Sara Sims > Graduate Research Fellow > University of Alabama at Birmingham > Department of Psychology > 205-975-4060 > sno...@uab.edu<mailto:sno...@uab.edu> > > On 3/19/19, 3:30 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D."<mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D.> <mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofdgr...@mgh.harvard.edu> wrote: > > I think the problem is that one or more of the subjects has all 0s. The > way mris_preproc works is that if any subject has a 0 in a vertex, that > vertex is set to 0 for all subjects. So, if one subject has all 0s or if > tp1=tp2, then everything can get set to 0. At the end of the terminal > output you'll see "Found 0 voxels in prune mask" indicating that this is > the case. I've created a version of mris_preproc that allows you to turn > this function off using --no-prune. You can get it from here: > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc > I would run it with --no-prune and without --paired-diff to give you a > stack of all data. You can load this as an overlay in freeview. At the > top of the freeview window is a little box with waveform in it. If you > click on that and then click on a point in the surface, you should be >
Re: [Freesurfer] mris_preproc not running
External Email - Use Caution
Doug,
I have implemented the new version of the command. I am getting this error when
I add the no-prune flag to my script.
ERROR: could not find volume --no-prune. Does it exist?
ERROR: reading --no-prune
Are there specifics with where in the command line it should go? I have tried
it near the beginning and near the end and still get this error.
Sara Sims
Graduate Research Fellow
University of Alabama at Birmingham
Department of Psychology
205-975-4060
sno...@uab.edu
On 3/19/19, 3:30 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Greve, Douglas N.,Ph.D." wrote:
I think the problem is that one or more of the subjects has all 0s. The
way mris_preproc works is that if any subject has a 0 in a vertex, that
vertex is set to 0 for all subjects. So, if one subject has all 0s or if
tp1=tp2, then everything can get set to 0. At the end of the terminal
output you'll see "Found 0 voxels in prune mask" indicating that this is
the case. I've created a version of mris_preproc that allows you to turn
this function off using --no-prune. You can get it from here:
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc
I would run it with --no-prune and without --paired-diff to give you a
stack of all data. You can load this as an overlay in freeview. At the
top of the freeview window is a little box with waveform in it. If you
click on that and then click on a point in the surface, you should be
able to see a waveform of the measurements for all inputs. See if there
is one that is always 0. If you don't find any, then repeat with
--paired-diff
On 3/19/19 3:30 PM, Sims, Sara A (Campus) wrote:
>
> External Email - Use Caution
>
> I uploaded them to the Filedrop here:
> http://gate.nmr.mgh.harvard.edu/filedrop2/?p=65zt2jk45ll
>
> Thanks!
>
> Sara Sims
>
> Graduate Research Fellow
>
> University of Alabama at Birmingham
>
> Department of Psychology
>
> 205-975-4060
>
> sno...@uab.edu
>
> *From: * on behalf of "Greve,
> Douglas N.,Ph.D."
> *Reply-To: *Freesurfer support list
> *Date: *Monday, March 18, 2019 at 10:24 AM
> *To: *"freesurfer@nmr.mgh.harvard.edu"
> *Subject: *Re: [Freesurfer] mris_preproc not running
>
>
> can you send the terminal output? I realize it might be quite big. You
> can ftp it to here: /autofs/space/nihilus_001/CICS/ACRsoftware/ACRcurrent
>
>
> On 3/18/19 11:12 AM, Sims, Sara A (Campus) wrote:
>
> *External Email - Use Caution *
>
> Hello!
>
> I have 786 subjects that I am trying to do a paired difference
> analysis using mri_glm. I am getting stuck at the mris_preproc
> stage. I have tried running it on a handful of subjects and it
> works wonderfully. However, when I run it on all the subjects it
> outputs an empty file.
>
> I think part of my problem is that I am having to do 1572 flags to
> enter all the subjects files (which I made a script to create, I
> did not hand type them). Is there a better way to do this? Do I
> just have too many subjects?
>
> This is what I have that isn’t working:
>
> *mris_preproc --target fsaverage --hemi lh --isp
> $in/${network}/100206.${run1}/lhsurf.mgh --isp
> $in/${network}/100206.${run2}/lhsurf.mgh --isp
> $in/${network}/100307.${run1}/lhsurf.mgh --isp
> $in/${network}/100307.${run2}/lhsurf.mgh ……. --out
> $out/preproc_${network}_${pair}/lh.paired-diff.${network}_${pair}.mgh
> --f $sublist --paired-diff --no-cortex-only*
>
> **
>
> Thanks for the help!
>
> Sara Sims
>
>
>
> ___
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] mris_preproc not running
External Email - Use Caution
I uploaded them to the Filedrop here:
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=65zt2jk45ll
Thanks!
Sara Sims
Graduate Research Fellow
University of Alabama at Birmingham
Department of Psychology
205-975-4060
sno...@uab.edu
From: on behalf of "Greve, Douglas
N.,Ph.D."
Reply-To: Freesurfer support list
Date: Monday, March 18, 2019 at 10:24 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] mris_preproc not running
can you send the terminal output? I realize it might be quite big. You can ftp
it to here: /autofs/space/nihilus_001/CICS/ACRsoftware/ACRcurrent
On 3/18/19 11:12 AM, Sims, Sara A (Campus) wrote:
External Email - Use Caution
Hello!
I have 786 subjects that I am trying to do a paired difference analysis using
mri_glm. I am getting stuck at the mris_preproc stage. I have tried running it
on a handful of subjects and it works wonderfully. However, when I run it on
all the subjects it outputs an empty file.
I think part of my problem is that I am having to do 1572 flags to enter all
the subjects files (which I made a script to create, I did not hand type them).
Is there a better way to do this? Do I just have too many subjects?
This is what I have that isn’t working:
mris_preproc --target fsaverage --hemi lh --isp
$in/${network}/100206.${run1}/lhsurf.mgh --isp
$in/${network}/100206.${run2}/lhsurf.mgh --isp
$in/${network}/100307.${run1}/lhsurf.mgh --isp
$in/${network}/100307.${run2}/lhsurf.mgh ……. --out
$out/preproc_${network}_${pair}/lh.paired-diff.${network}_${pair}.mgh --f
$sublist --paired-diff --no-cortex-only
Thanks for the help!
Sara Sims
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] mris_preproc not running
External Email - Use Caution
Hello!
I have 786 subjects that I am trying to do a paired difference analysis using
mri_glm. I am getting stuck at the mris_preproc stage. I have tried running it
on a handful of subjects and it works wonderfully. However, when I run it on
all the subjects it outputs an empty file.
I think part of my problem is that I am having to do 1572 flags to enter all
the subjects files (which I made a script to create, I did not hand type them).
Is there a better way to do this? Do I just have too many subjects?
This is what I have that isn’t working:
mris_preproc --target fsaverage --hemi lh --isp
$in/${network}/100206.${run1}/lhsurf.mgh --isp
$in/${network}/100206.${run2}/lhsurf.mgh --isp
$in/${network}/100307.${run1}/lhsurf.mgh --isp
$in/${network}/100307.${run2}/lhsurf.mgh ……. --out
$out/preproc_${network}_${pair}/lh.paired-diff.${network}_${pair}.mgh --f
$sublist --paired-diff --no-cortex-only
Thanks for the help!
Sara Sims
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