Re: [Freesurfer] -qcache error

[Tadashi Shiohama]

External Email - Use Caution

Hi Dr. Greve,

I found out the reason why it does not work.
That was because the subjects' folder does not include lh white.K. Thank you so 
much!

Tadashi Shiohama

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas 
N.,Ph.D.
Sent: Friday, January 4, 2019 4:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] -qcache error

Does that file exist? If not, check to see whether that subject finished or 
whether there was an error

On 12/20/18 2:37 PM, 塩浜 直 wrote:
>  External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I'm attempting to do group analysis for cortical thickness map using Qdec GUI.
> We've already have recon-all files that were made by “recon-all –s 
> subjid –i subjid.nii –all” on other Linux OS 
> (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0)
>
> Firstly, I try to run command “recon-all –s subject –qcache” for each subject 
> floders.
> However, the program stopped with error 1 minutes after starting.
> Last line of recon-all.log showed as follows.
>
> #@# Qdec
> Cache preproc lh white.K fsaverage Thu Dec 20 12:03:25 EST 2018 
> /Users/emitakahashi/freesurfer/subjects/ASD001/surf
> \n
> mris_preproc --s ASD001 --hemi lh --meas white.K --target fsaverage 
> --out lh.white.K.fsaverage.mgh \n nsubjects = 1
> ERROR:
> cannot find 
> /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.white.K
> Darwin
> emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 
> 22
> 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64
>
> I've searched the list but I can find no similar errors have been 
> reported. Does anyone have any thoughts on how to trouble-shoot this 
> one? Also, Ive attached the recon-all.log in case it's of any use.
> 1) FreeSurfer version: Free Surfer 6.0
> 2) Platform: macOS Mojave (64b Intel)
> 3) recon-all.log: see attached
>
> Tadashi Shiohama
>
> ___
> Freesurfer mailing list
> 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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] map parcellations into DWI space?

[Yerong Li]

External Email - Use Caution

Yes, this is super-helpful. Thank you so much.

Yerong
Quoting "Greve, Douglas N.,Ph.D." :

> you might try this page
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0
>
> On 12/30/18 1:45 AM, Yerong Li wrote:
>> External Email - Use Caution
>> Dear FreeSurfer experts:
>>  I am trying to map ./mri/aparc.a2009s+aseg.mgz and
>> ./mri/aparc+aseg.mgz into DTI file.
>>  Let's say, we have a DTI file with its b-vectors:
>>     ./bvals
>>     ./bvecs
>>     ./data.nii.gz
>>
>>   I am trying to use the command from this webpage:
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
>>
>>   So I used the command :
>>     mri_label2vol --seg aparc+aseg.mgz --temp ./data.nii.gz  --o
>> dk-in-rawavg.mgz --regheader aparc+aseg.mgz
>>
>>   The output file seems not very reasonable. Could you help me with this?
>>
>> Yerong
>> ==
>> Can you be more specific about which files you want to map into your DWI
>> space? Eg, if you want to map wmparc.mgz, then use mri_label2vol. You
>> will need a registration file which you can obtain with bbregister
>>
>>
>> On 12/05/2018 02:34 AM, Maedeh Khalilian wrote:
>>>
>>>     External Email - Use Caution
>>>
>>> Dear FreeSurfer experts,
>>> I have a parcellation  and a whole brain white matter files which are
>>> the outputs of FreeSurfer.
>>> I want to register them to my DWI. I mean I want my parcellation and
>>> white matter to be in the physical space of my DWI.
>>> Can FreeSurfer do it for me?
>>> If not , can you suggest me a toolbox that can do it fast?
>>> I would be grateful if u could help me.
>>> Cheers,
>>> Maedeh,
>>>
>>>
>>
>
>
>
> 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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] MRI sequence parameter difference and effect on cortical thickness values

[Arsenije Subotic]

External Email - Use Caution

Dear experts,

For our study, we are planning on combining two different datasets to examine 
cortical thickness. There is a slight difference in the inversion time (400 vs 
650) and flip angle ( 8 vs 11) between the two datasets. I know that free 
surfer measurements are fairly consistent across different scanner types and 
strengths, but do you know if slight differences in mri sequence parameters 
have an affect on cortical thickness? I was planning on adding it as a 
covariate in our analysis just in case.

Thank you!
Arsenije

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Diagnosing a recon error

[Greve, Douglas N.,Ph.D.]

Do you have access to the stderr output from this process?

On 1/3/19 3:55 PM, Maksimovskiy, Arkadiy wrote:
>
> Dear Experts,
>
> I was wondering if someone might be able to help diagnose a recon error.
>
> I used the following command to initiate recon:
>
> recon-all -subject RMD002 -i 
> /ncf/anl/anl01/MultiMode/Data/structural/T1_MEMPRAGE_5_RMD002_e1.nii 
> -T2 /ncf/anl/anl01/MultiMode/Data/structural/T2_SPACE_6_RMD002.nii 
> -T2pial -3T -all
>
> The recon log indicates an error: recon-all -s RMD002 exited with ERRORS
>
> Attached is the log file. I used grep to search through it for 
> “failed” or “error”, but am unable to see any indices of errors, other 
> than this message at the bottom of the log.
>
> I would love to hear any info for what might have gone wrong.
>
> Thank you for all your help,
>
> Arkadiy
>
>
> ___
> Freesurfer mailing list
> 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] Diagnosing a recon error

[Maksimovskiy, Arkadiy]

Dear Experts,

I was wondering if someone might be able to help diagnose a recon error.

I used the following command to initiate recon:

recon-all -subject RMD002 -i 
/ncf/anl/anl01/MultiMode/Data/structural/T1_MEMPRAGE_5_RMD002_e1.nii -T2 
/ncf/anl/anl01/MultiMode/Data/structural/T2_SPACE_6_RMD002.nii -T2pial -3T -all

The recon log indicates an error: recon-all -s RMD002 exited with ERRORS

Attached is the log file. I used grep to search through it for “failed” or 
“error”, but am unable to see any indices of errors, other than this message at 
the bottom of the log.

I would love to hear any info for what might have gone wrong.
Thank you for all your help,
Arkadiy


recon-all.log
Description: recon-all.log
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Extracting cortical thickness from a significant cluster in an independent sample

[Tamara Sussman]

External Email - Use Caution

Thank you so much, Douglas, it works!!

On Thu, Jan 3, 2019 at 3:10 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

>
> The first command does not work because --slabel requires three options
> and it is interpreting "--i" and "/Volumes...mgh" as those two so it
> thinks you have not included. It is probably better to use something like
> mri_segstats --seg ocn.mgh --excludeid 0 --avgwf test.dat
> --sumTest_SupParietal.sum --i lh.thickness.fwhm10.fsaverage.mgh
>
>
> On 1/3/19 2:41 PM, Tamara Sussman wrote:
> >
> > External Email - Use Caution
> >
> > Thanks so much for your suggestion, Douglas.
> > Here is the whole input and output:
> >
> > Tamara-Posner-lab:~ posnerlab$ mri_segstats --slabel
> >
> /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
>
> >
> --i/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh
>
> > --nonempty --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum
> >
> > ERROR: cannot do frame average without input volume
> >
> >
> > I was using --slabel instead of --seg because I am using surfaces, and
> > not volumes. Just to test it out, I tried using the --seg aseg too,
> > and got the same error:
> >
> > Tamara-Posner-lab:~ posnerlab$ mri_segstats --seg
> >
> /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/mri/aseg.mgz
>
> > --mask
> >
> /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
>
> > --nonempty --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum
> >
> > ERROR: cannot do frame average without input volume
> >
> > Thank you again for your help!
> > Tamara
> >
> >
> > On Thu, Jan 3, 2019 at 1:59 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > Can you include the full command line (no $variables) and the full
> > terminal output?
> >
> > On 1/2/19 4:22 PM, Tamara Sussman wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Thanks for your response - yes, I should have included this
> > > information before. :)
> > >
> > > $label was set to a label I made by 1. binarizing the cluster
> > results
> > > from the previous analysis, and then 2. using mri_vol2label to
> > convert
> > > this into a label
> > >
> > >
> >
>  
> label=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
> > >
> > >
> > > $input was set to an individual's thickness data (analogous data
> > that
> > > I used in the initial analysis):
> > >
> >
>  
> input=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh
> > >
> > > On Wed, Jan 2, 2019 at 4:09 PM  > 
> > > >> wrote:
> > >
> > >   External Email - Use Caution
> > >
> > > What are $label and $input set to?
> > >
> > > > On January 2, 2019 at 9:13 PM Tamara Sussman
> > mailto:tsuss...@gmail.com>
> > > >>
> wrote:
> > > >
> > > >
> > > > External Email - Use Caution
> > > >
> > > > Hello Freesurfer Experts!
> > > >
> > > > Thank you in advance for considering this question.
> > > >
> > > > I did a cortical thickness analysis (surface-based), and
> > found a
> > > > significant cluster. I found the average cortical
> > thickness in*
> > > this group*,
> > > > in the .*y.ocn.dat* file, which is great.
> > > >
> > > > Now I want to find the average cortical thickness in the same
> > > cluster, in a
> > > > separate group of subjects.
> > > >
> > > > I tried using mri_segstats, but it doesn't seem to work:
> > > >
> > > > mri_segstats --slabel $label --i $input --nonempty
> --excludeid
> > > 0 --avgwf
> > > > test.dat --sum  Test_SupParietal.sum
> > > >
> > > > The error I am getting is:
> > > >
> > > > ERROR: cannot do frame average without input volume
> > > >
> > > > Any thoughts about a better way to approach this analysis?
> > > >
> > > > Thanks again in advance!
> > > > -T
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > >  > 

Re: [Freesurfer] Extracting cortical thickness from a significant cluster in an independent sample

[Greve, Douglas N.,Ph.D.]

The first command does not work because --slabel requires three options 
and it is interpreting "--i" and "/Volumes...mgh" as those two so it 
thinks you have not included. It is probably better to use something like
mri_segstats --seg ocn.mgh --excludeid 0 --avgwf test.dat 
--sumTest_SupParietal.sum --i lh.thickness.fwhm10.fsaverage.mgh


On 1/3/19 2:41 PM, Tamara Sussman wrote:
>
> External Email - Use Caution
>
> Thanks so much for your suggestion, Douglas.
> Here is the whole input and output:
>
> Tamara-Posner-lab:~ posnerlab$ mri_segstats --slabel 
> /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
>  
> --i/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh
>  
> --nonempty --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum
>
> ERROR: cannot do frame average without input volume
>
>
> I was using --slabel instead of --seg because I am using surfaces, and 
> not volumes. Just to test it out, I tried using the --seg aseg too, 
> and got the same error:
>
> Tamara-Posner-lab:~ posnerlab$ mri_segstats --seg 
> /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/mri/aseg.mgz
>  
> --mask 
> /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
>  
> --nonempty --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum
>
> ERROR: cannot do frame average without input volume
>
> Thank you again for your help!
> Tamara
>
>
> On Thu, Jan 3, 2019 at 1:59 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Can you include the full command line (no $variables) and the full
> terminal output?
>
> On 1/2/19 4:22 PM, Tamara Sussman wrote:
> >
> > External Email - Use Caution
> >
> > Thanks for your response - yes, I should have included this
> > information before. :)
> >
> > $label was set to a label I made by 1. binarizing the cluster
> results
> > from the previous analysis, and then 2. using mri_vol2label to
> convert
> > this into a label
> >
> >
> 
> label=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
> >
> >
> > $input was set to an individual's thickness data (analogous data
> that
> > I used in the initial analysis):
> >
> 
> input=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh
> >
> > On Wed, Jan 2, 2019 at 4:09 PM  
> > >> wrote:
> >
> >           External Email - Use Caution
> >
> >     What are $label and $input set to?
> >
> >     > On January 2, 2019 at 9:13 PM Tamara Sussman
> mailto:tsuss...@gmail.com>
> >     >> wrote:
> >     >
> >     >
> >     >         External Email - Use Caution
> >     >
> >     > Hello Freesurfer Experts!
> >     >
> >     > Thank you in advance for considering this question.
> >     >
> >     > I did a cortical thickness analysis (surface-based), and
> found a
> >     > significant cluster. I found the average cortical
> thickness in*
> >     this group*,
> >     > in the .*y.ocn.dat* file, which is great.
> >     >
> >     > Now I want to find the average cortical thickness in the same
> >     cluster, in a
> >     > separate group of subjects.
> >     >
> >     > I tried using mri_segstats, but it doesn't seem to work:
> >     >
> >     > mri_segstats --slabel $label --i $input --nonempty --excludeid
> >     0 --avgwf
> >     > test.dat --sum  Test_SupParietal.sum
> >     >
> >     > The error I am getting is:
> >     >
> >     > ERROR: cannot do frame average without input volume
> >     >
> >     > Any thoughts about a better way to approach this analysis?
> >     >
> >     > Thanks again in advance!
> >     > -T
> >     > ___
> >     > Freesurfer mailing list
> >     > Freesurfer@nmr.mgh.harvard.edu
> 
> >      >
> >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >     --
> >     Dr. Tim Schäfer
> >     Postdoc Computational Neuroimaging
> >     Department of Child and Adolescent Psychiatry,
> Psychosomatics and
> >     Psychotherapy
> >     University Hospital Frankfurt, Goethe University Frankfurt am
> >     Main, Germany
> >

Re: [Freesurfer] Extracting cortical thickness from a significant cluster in an independent sample

[Tamara Sussman]

External Email - Use Caution

Thanks so much for your suggestion, Douglas.

Here is the whole input and output:

Tamara-Posner-lab:~ posnerlab$ mri_segstats --slabel
/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
--i  
/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh
--nonempty --excludeid 0 --avgwf test.dat --sum  Test_SupParietal.sum

ERROR: cannot do frame average without input volume

I was using --slabel instead of --seg because I am using surfaces, and not
volumes. Just to test it out, I tried using the --seg aseg too, and got the
same error:

Tamara-Posner-lab:~ posnerlab$ mri_segstats --seg
/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/mri/aseg.mgz
--mask
/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
--nonempty --excludeid 0 --avgwf test.dat --sum  Test_SupParietal.sum

ERROR: cannot do frame average without input volume

Thank you again for your help!
Tamara


On Thu, Jan 3, 2019 at 1:59 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Can you include the full command line (no $variables) and the full
> terminal output?
>
> On 1/2/19 4:22 PM, Tamara Sussman wrote:
> >
> > External Email - Use Caution
> >
> > Thanks for your response - yes, I should have included this
> > information before. :)
> >
> > $label was set to a label I made by 1. binarizing the cluster results
> > from the previous analysis, and then 2. using mri_vol2label to convert
> > this into a label
> >
> >
> label=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
> >
> >
> > $input was set to an individual's thickness data (analogous data that
> > I used in the initial analysis):
> >
> input=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh
> >
> > On Wed, Jan 2, 2019 at 4:09 PM  > > wrote:
> >
> >   External Email - Use Caution
> >
> > What are $label and $input set to?
> >
> > > On January 2, 2019 at 9:13 PM Tamara Sussman  > > wrote:
> > >
> > >
> > > External Email - Use Caution
> > >
> > > Hello Freesurfer Experts!
> > >
> > > Thank you in advance for considering this question.
> > >
> > > I did a cortical thickness analysis (surface-based), and found a
> > > significant cluster. I found the average cortical thickness in*
> > this group*,
> > > in the .*y.ocn.dat* file, which is great.
> > >
> > > Now I want to find the average cortical thickness in the same
> > cluster, in a
> > > separate group of subjects.
> > >
> > > I tried using mri_segstats, but it doesn't seem to work:
> > >
> > > mri_segstats --slabel $label --i $input  --nonempty --excludeid
> > 0 --avgwf
> > > test.dat --sum  Test_SupParietal.sum
> > >
> > > The error I am getting is:
> > >
> > > ERROR: cannot do frame average without input volume
> > >
> > > Any thoughts about a better way to approach this analysis?
> > >
> > > Thanks again in advance!
> > > -T
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Dr. Tim Schäfer
> > Postdoc Computational Neuroimaging
> > Department of Child and Adolescent Psychiatry, Psychosomatics and
> > Psychotherapy
> > University Hospital Frankfurt, Goethe University Frankfurt am
> > Main, Germany
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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 mailing list
> 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

Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047

[Boyd, Emma]

Hi Jeongson,


I took a look at your data, thank you for uploading it. Your recon is likely 
failing because your case has a large pathology that is causing your white 
matter surface to be topologically incorrect. I recommend filling in that whole 
area on the wm.mgz mask and re-running the rest of your recon using the 
instructions on the page below.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0


Please let us know if you have questions, or if your recon still fails after 
these edits.

Best,

Emma


Emma Boyd
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Friday, December 21, 2018 12:13:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error : Too many intersected faces for face 
120047

did you try to load it as a surface? If you want to upload the entire
subject dir (tarred and gzipped) to our ftp site we will take a look. In
the meantime you can also just post an image of the volume in 3 planes,
that might help

cheers
Bruce
On Fri, 21 Dec 2018, 허정선 wrote:

>External Email - Use Caution
>
> Thank you for your reply.
>
> Is it impossible with 2mm? Unfortunately, the data we collect for the study 
> all have same thickness of voxel.
> And, there was a problem like the photo below, and only the recon-all.log 
> could be attached to you.
>
>
> Thanks,
> Jeongson
> --
>
> Message: 1
> Date: Thu, 20 Dec 2018 10:13:16 -0500 (EST)
> From: Bruce Fischl 
> Subject: Re: [Freesurfer] recon-all error : Too many intersected faces
>for face 120047 (60827, 60826, 59444)
> To: Freesurfer support list 
> Message-ID:
>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Jeongson
>
> it certainly looks like something went badly wrong. 2mm may be too thick
> - we typically recommend <=1.5mm for any voxel direction. Can you send us
> the recon-all.log? And maybe a snapshot of the volume with the
> lh.orig.nofix and rh.orig.nofix overlaid?
>
> cheers
> Bruce
>
>
> On Thu, 20 Dec
> 2018, ??? wrote:
>
>>External Email - Use Caution
>>
>> Hello Freesurfer developers
>> I'm starting using FS and I have a problem running recon-all.
>> #recon-all -s /usr/local/freesurfer/subjects/20180108 -all
>> I've attached the output to a ERROR image file.
>>
>> We're doing on a GE scanner 3T, T1-FSPGR axial slices, 3D with a slice 
>> thickness of 2.0mm.
>> freesurfer version : freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
>>
>> Any help is greatly appreciated.
>>
>> Thanks.
>>
>> Jeongson
>
> --
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] -qcache error

[Greve, Douglas N.,Ph.D.]

Does that file exist? If not, check to see whether that subject finished 
or whether there was an error

On 12/20/18 2:37 PM, 塩浜 直 wrote:
>  External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I'm attempting to do group analysis for cortical thickness map using Qdec GUI.
> We've already have recon-all files that were made by “recon-all –s subjid –i 
> subjid.nii
> –all” on other Linux OS (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0)
>
> Firstly, I try to run command “recon-all –s subject –qcache” for each subject 
> floders.
> However, the program stopped with error 1 minutes after starting.
> Last line of recon-all.log showed as follows.
>
> #@# Qdec
> Cache preproc lh white.K fsaverage Thu Dec 20 12:03:25 EST 2018
> /Users/emitakahashi/freesurfer/subjects/ASD001/surf
> \n
> mris_preproc --s ASD001 --hemi lh --meas white.K --target fsaverage --out
> lh.white.K.fsaverage.mgh \n
> nsubjects
> = 1
> ERROR:
> cannot find /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.white.K
> Darwin
> emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22
> 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64
>
> I've searched the list but I can find no similar errors have been reported. 
> Does
> anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached
> the recon-all.log in case it's of any use.
> 1) FreeSurfer version: Free Surfer 6.0
> 2) Platform: macOS Mojave (64b Intel)
> 3) recon-all.log: see attached
>
> Tadashi Shiohama
>
> ___
> Freesurfer mailing list
> 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

Re: [Freesurfer] map parcellations into DWI space?

[Greve, Douglas N.,Ph.D.]

you might try this page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0

On 12/30/18 1:45 AM, Yerong Li wrote:
> External Email - Use Caution
> Dear FreeSurfer experts:
>  I am trying to map ./mri/aparc.a2009s+aseg.mgz and 
> ./mri/aparc+aseg.mgz into DTI file.
>  Let's say, we have a DTI file with its b-vectors:
>     ./bvals
>     ./bvecs
>     ./data.nii.gz
>
>   I am trying to use the command from this webpage: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
>
>   So I used the command :
>     mri_label2vol --seg aparc+aseg.mgz --temp ./data.nii.gz  --o 
> dk-in-rawavg.mgz --regheader aparc+aseg.mgz
>
>   The output file seems not very reasonable. Could you help me with this?
>
> Yerong
> ==
> Can you be more specific about which files you want to map into your DWI
> space? Eg, if you want to map wmparc.mgz, then use mri_label2vol. You
> will need a registration file which you can obtain with bbregister
>
>
> On 12/05/2018 02:34 AM, Maedeh Khalilian wrote:
>>
>>     External Email - Use Caution
>>
>> Dear FreeSurfer experts,
>> I have a parcellation  and a whole brain white matter files which are 
>> the outputs of FreeSurfer.
>> I want to register them to my DWI. I mean I want my parcellation and 
>> white matter to be in the physical space of my DWI.
>> Can FreeSurfer do it for me?
>> If not , can you suggest me a toolbox that can do it fast?
>> I would be grateful if u could help me.
>> Cheers,
>> Maedeh,
>>
>>
>


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Which T1 volume to use for coregistration with PET volume

[Matthieu Vanhoutte]

External Email - Use Caution

Thank you Douglas for this clarification.

So, correction of inhomogeneities and intensity normalization would have no 
positive effect on the PET/MR coregistration ?

Best,
Matt

> Le 3 janv. 2019 à 20:04, Greve, Douglas N.,Ph.D.  a 
> écrit :
> 
> I doubt it would make much difference. If your PET has lots of 
> extracerebral uptake, then I might use something that has not been skull 
> stripped (eg, orig.mgz, T1.mgz, nu.mgz). If it does not  have much 
> extracerebral, then using brain.mgz is probably better.
> 
> On 12/31/18 10:53 AM, Bruce Fischl wrote:
>> HI Matt
>> 
>> yes, I would agree, but Doug will give you the definitive answer
>> 
>> cheers
>> Bruce
>> On Fri, 28 Dec 2018, Matthieu Vanhoutte wrote:
>> 
>>>External Email - Use Caution
>>> 
>>> Dear Freesurfer’s experts,
>>> 
>>> I used mri_coreg command to coregister PET image onto T1 volume. 
>>> Basically, this command coregister PET image onto orig.mgz volume 
>>> (default target). However, I wonder if T1.mgz wouldn’t be a better 
>>> target since it has been corrected for inhomogeneities and intensity 
>>> normalized ?
>>> 
>>> Thanks for helping !
>>> 
>>> Best,
>>> Matt
>>> 
>>> ___
>>> Freesurfer mailing list
>>> 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 mailing list
> 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

Re: [Freesurfer] FSGD file

[Greve, Douglas N.,Ph.D.]

The contrast is not correct for your design. Your design matrix will 
have 3 columns, one for HC, one for CMT, and one for 
rh.thickness_30.fsavg.mgh. Ie, it automatcailly interprets PVRs in a 
DOSS kind of way. If you want to test for a difference in 
thickness-meylin slopes between the two groups, you will need to have 
two PVRs, one where the value is the thickness for HC subjects and 0 for 
CMT subjects, the other the reverse, then set your contrast to 0 0 1 -1. 
If you just want to remove thickness as a nuisance, then you can stick 
with what you have and just use a contrast of 1 -1 0

On 12/25/18 5:05 AM, Raffaele Dubbioso wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer team,
>
> I'm running a group analysis where I'd like to compare myelination 
> between two groups regressing out cortical thickness.
> Unfortunately I get always the same error message:
> dimension mismatch between X and contrast group.diff.mtx       X has 3 
> cols, C has 4 cols. Is my group.mtx correct?
>
> My command line is:
> mri_glmfit --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd 
> thickness.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --C 
> group-x-thick --Cg1g2.intercept.mts --C g1g2.thick.mtx --surf 
> fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness.glmdir
>
> My group_diff.mtx: 1 -1 0 0
>
> This is my FSGD FILE:
> GroupDescriptorFile 1
> Title Myelin
> Class HC
> Class CMT
> Inputfs_VFHC
> 
>
>
>  Thank you very much for your help
>
> Best regards,
> Raffaele
>
> ___
> Freesurfer mailing list
> 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

Re: [Freesurfer] Which T1 volume to use for coregistration with PET volume

[Greve, Douglas N.,Ph.D.]

I doubt it would make much difference. If your PET has lots of 
extracerebral uptake, then I might use something that has not been skull 
stripped (eg, orig.mgz, T1.mgz, nu.mgz). If it does not  have much 
extracerebral, then using brain.mgz is probably better.

On 12/31/18 10:53 AM, Bruce Fischl wrote:
> HI Matt
>
> yes, I would agree, but Doug will give you the definitive answer
>
> cheers
> Bruce
> On Fri, 28 Dec 2018, Matthieu Vanhoutte wrote:
>
>>    External Email - Use Caution
>>
>> Dear Freesurfer’s experts,
>>
>> I used mri_coreg command to coregister PET image onto T1 volume. 
>> Basically, this command coregister PET image onto orig.mgz volume 
>> (default target). However, I wonder if T1.mgz wouldn’t be a better 
>> target since it has been corrected for inhomogeneities and intensity 
>> normalized ?
>>
>> Thanks for helping !
>>
>> Best,
>> Matt
>>
>> ___
>> Freesurfer mailing list
>> 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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Extracting cortical thickness from a significant cluster in an independent sample

[Greve, Douglas N.,Ph.D.]

Can you include the full command line (no $variables) and the full 
terminal output?

On 1/2/19 4:22 PM, Tamara Sussman wrote:
>
> External Email - Use Caution
>
> Thanks for your response - yes, I should have included this 
> information before. :)
>
> $label was set to a label I made by 1. binarizing the cluster results 
> from the previous analysis, and then 2. using mri_vol2label to convert 
> this into a label
>
> label=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
>
>
> $input was set to an individual's thickness data (analogous data that 
> I used in the initial analysis): 
> input=/Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T2/AN_Klarman_AN_T2_23/surf/lh.thickness.fwhm10.fsaverage.mgh
>
> On Wed, Jan 2, 2019 at 4:09 PM  > wrote:
>
>       External Email - Use Caution
>
> What are $label and $input set to?
>
> > On January 2, 2019 at 9:13 PM Tamara Sussman  > wrote:
> >
> >
> >         External Email - Use Caution
> >
> > Hello Freesurfer Experts!
> >
> > Thank you in advance for considering this question.
> >
> > I did a cortical thickness analysis (surface-based), and found a
> > significant cluster. I found the average cortical thickness in*
> this group*,
> > in the .*y.ocn.dat* file, which is great.
> >
> > Now I want to find the average cortical thickness in the same
> cluster, in a
> > separate group of subjects.
> >
> > I tried using mri_segstats, but it doesn't seem to work:
> >
> > mri_segstats --slabel $label --i $input  --nonempty --excludeid
> 0 --avgwf
> > test.dat --sum  Test_SupParietal.sum
> >
> > The error I am getting is:
> >
> > ERROR: cannot do frame average without input volume
> >
> > Any thoughts about a better way to approach this analysis?
> >
> > Thanks again in advance!
> > -T
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am
> Main, Germany
>
> ___
> Freesurfer mailing list
> 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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] run preproc-sess wrongly and some other question about FSFAST

[Greve, Douglas N.,Ph.D.]

On 1/3/19 5:07 AM, xi star wrote:
>
> External Email - Use Caution
>
> dear experts,
> I try to run FSFAST with a block design paradigm. there a few question 
> i can figure out on my own.
> the 1st question:
> the directory structure was set as:
> -meridian
>      --sess01
>            --bold
>                  -001
>                  -002
>            --lpx (subjectname folder contian anatomical data run by 
> "recon-all" previously)
>            --subjectname (a file)
> Since there was only one subject, i didn't create sessid.
> then i run:
> preproc-sess -s sess01 -fsd bold -per-run -fwhm 5 -sliceorder odd 
> -surface fsaverage lhrh -init-fsl
> but i got this warning (the full log is in the attachment):
>
> if: Expression Syntax.
>
> I wonder what's wrong with the command.
>
I'm not sure. What version of FS are you running? If version 6, then 
don't use -init-fsl. If the error persists, then run it with -debug as 
the first option and send the terminal output.
>
> --
>
> the 2nd question:
>
> following the website 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastLinkAnatData
>
> I create a subjectname file which contains:
>
> cd $SUBJECTS_DIR/$SUBJECT
>
> echo "$SUBJECT">>lpx
>
> is it work? How to link the functional data to anatomical data?
>
I actually don't know what that refers to. That page is way out of date 
(I just deleted it). An "lpx" file is not needed.
>
> --
>
> the 3rd question:
>
> i use a stationary wedge stimuli to activate the horizontal and 
> vertical meridian representations in visual cortex. the design 
> parameters: TR=2, 8hz flickering checkerbords, 16s fixation followed 
> by 4 conditions（20s each）, each condition show a wedge in up, down, 
> left and right meridian, 3 repetitions
>
> the meridian.par was set as:
>
> 0.0 016.01.0fix
>
> 17.0120.01.0up
>
> 37.0220.01.0down
>
> 57.0320.01.0left
>
> 77.0420.01.0right
>
> 97.0120.01.0up
>
> 117.0220.01.0down
>
> 137.0320.01.0left
>
> 157.0420.01.0right
>
> 177.0120.01.0up
>
> 197.0220.01.0down
>
> 217.0320.01.0left
>
> 237.0420.01.0right
>
> my question is, in the first-level analysis, is right to write the 
> command:
>
> mkanalysis-sess \
> -analysis meridian \
> -event-related -paradigm meridian.par \
> -TR 2 -nconditions 4 \
> -mcextreg
Yes, that looks correct
>
> best,
>
> star
>
>
>
> ___
> Freesurfer mailing list
> 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] run preproc-sess wrongly and some other question about FSFAST

[xi star]

External Email - Use Caution

dear experts,
I try to run FSFAST with a block design paradigm. there a few question i
can figure out on my own.
the 1st question:
the directory structure was set as:
-meridian
 --sess01
   --bold
 -001
 -002
   --lpx (subjectname folder contian anatomical data run by
"recon-all" previously)
   --subjectname (a file)
Since there was only one subject, i didn't create sessid.
then i run:
preproc-sess -s sess01 -fsd bold -per-run -fwhm 5 -sliceorder odd -surface
fsaverage lhrh -init-fsl
but i got this warning (the full log is in the attachment):

if: Expression Syntax.

I wonder what's wrong with the command.

--

the 2nd question:

following the website
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastLinkAnatData

I create a subjectname file which contains:

cd $SUBJECTS_DIR/$SUBJECT

echo "$SUBJECT">>lpx


is it work? How to link the functional data to anatomical data?

--

the 3rd question:

i use a stationary wedge stimuli to activate the horizontal and vertical
meridian representations in visual cortex. the design parameters: TR=2, 8hz
flickering checkerbords, 16s fixation followed by 4 conditions（20s each）,
each condition show a wedge in up, down, left and right meridian, 3
repetitions

the meridian.par was set as:

0.0   0  16.0  1.0  fix

17.0  1  20.0  1.0  up

37.0  2  20.0  1.0  down

57.0  3  20.0  1.0  left

77.0  4  20.0  1.0  right

97.0  1  20.0  1.0  up

117.0  2  20.0  1.0  down

137.0  3  20.0  1.0  left

157.0  4  20.0  1.0  right

177.0  1  20.0  1.0  up

197.0  2  20.0  1.0  down

217.0  3  20.0  1.0  left

237.0  4  20.0  1.0  right


my question is, in the first-level analysis, is right to write the command:
mkanalysis-sess \
-analysis meridian \
-event-related -paradigm meridian.par \
-TR 2 -nconditions 4 \
-mcextreg

best,


star


preproc-sess.sess01.log.old
Description: Binary data
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer