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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 <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_binarize
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <9d91f7ea-a55b-cd78-2b55-687cf2078a8b@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
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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------------------------------
Message: 2
Date: Mon, 4 Dec 2017 12:32:00 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Clarification about "Per-Run" Motion
Correction and Registration in Preproc-Sess
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <813a5a08-d27e-a2a6-8472-66f998aaa4a2@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:
>
> 1) Why is this the preferred option instead of per-session?
The interpolation is less if it is done on a per-run basis, and the
registration might be better
> 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?
That is why we resample into the group atlas space (eg, fsaverage) or
the self anatomical space so that all the runs are aligned.
>
> Thank you very much,
>
> JohnMark
>
>
> _______________________________________________
> 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
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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------------------------------
Message: 3
Date: Mon, 4 Dec 2017 12:33:46 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freesurfer design
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <daca7a06-f2e5-09a1-f05b-7e24204bc8cb@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=windows-1252; format=flowed
In theory, this is just a two "group" analysis. Search the wiki for FSGD
to get examples. You can include covariates, but you must use a DOSS
model when running mri_glmfit
On 12/04/2017 04:41 AM, Dijkshoorn, A.B.C. (Aicha) wrote:
>
> Dear freesurfer group,
>
> I have two questions:
>
> Can I compare one patient with a created control group in Freesurfer
> on the following outcome measures: cortical thickness, brain volume
> and gyrification? If so, how can you?visualise that?
> When you do the cortical analysis with freesurfer?can?you?account
> for?covariates in the statistical model (before visualisation)?
>
> Kind regards,
>
> Aicha Dijkshoorn
>
>
>
> _______________________________________________
> 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
greve@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: 4
Date: Mon, 4 Dec 2017 12:39:55 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] subcortical structures volume
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <cb08cf9c-9912-c39e-8979-ace86c2ea5f4@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=UTF-8; format=flowed
Yes, you should take those into account. Not sure what you mean by
"which stat analysis".
On 12/01/2017 07:50 PM, ??? wrote:
> Hi professor,
>
> ? ?I am using Freesurfer 6.0 and get the volume of subcortical
> structures. I want to get the relationship between age and volume. I
> only have one group, is it necessary to take gender and ?eTIV as a
> covariate? If it is necessary, Which statistical analysis should be used?
> ? ?I really appreciate your help. Thanks a lot.
>
> Sincerely,
> Zheng
>
>
>
>
> _______________________________________________
> 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
greve@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: 5
Date: Mon, 4 Dec 2017 12:46:27 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_vol2surf wrong hemisphere
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <4ddc19b2-a602-5560-9cf5-0d7ff60baca5@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=windows-1252; format=flowed
How do you know what is right and left in the volume?
On 12/01/2017 01:59 PM, Defenderfer, Matthew K wrote:
>
> Hi,
>
> I have a strange issue I can't figure out. I am currently trying to
> use the parcellation from Gordon et al. 2014
> (http://www.nil.wustl.edu/labs/petersen/Resources.html ) to create ROIs
> for the frontoparietal network. They provided a volume of the
> parcellation in MNI152 space for public use. I took this volume and
> applied the mri_vol2surf command to it to create 2 overlays of the
> parcels, 1 for each hemisphere. The code was:
>
> mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage
> --mni152reg --o lh.Parcels_fsaverage_111.mgh --hemi lh
>
> mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage
> --mni152reg --o rh.Parcels_fsaverage_111.mgh --hemi rh
>
> The code ran, but the LH parcels in the volume were transferred to the
> RH on the surface and vice versa. This is a problem since the
> parcellation is not symmetric across hemispheres.This is not a problem
> with the volume either as I looked at it overlayed with the MNI152
> brain in fslview and saw that the parcels were on the correct
> hemisphere. Another problem is that 1 of the frontoparietal parcels,
> number 24, was not found on the surface of either hemisphere after
> turning it to a surface. I don't know why this would be the case since
> there are all cortical parcels.
>
> I have also tried this with a volume ROI that is only located on the
> left hemisphere. After running essentially the same vol2surf command
> as above, the ROI only appeared on the RH surface. I am using
> mri_vol2surf from Freesurfer v6.0.0
>
>
> Any help would be greatly appreciated. Thank you!
>
> Best,
> Matthew Defenderfer
>
>
> *Matthew K. Defenderfer B.S. |?Graduate Research Assistant*
>
> Graduate Biomedical Sciences|Neuroscience
>
> UAB?|?The University of Alabama at Birmingham
>
> Laboratory of Kristina Visscher, PhD
>
> Department of Neurobiology
>
> CIRC 111 | C: (865) 805-6389
>
>
>
>
> _______________________________________________
> 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
greve@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: 6
Date: Mon, 4 Dec 2017 12:47:18 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Concatenating .mgh surface space functional
MRI runs
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <6e8749cf-4be8-04c4-17a2-5b6a96d7a520@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=utf-8; format=flowed
mri_concat file1 file2 ... --o concatfile.mgh
On 11/30/2017 01:28 PM, Abisan - wrote:
> Hi Freesurfer experts,
>
> I want to concatenate multiple preprocessed fMRI runs in the form of
> .mgh freesurfer surface space files (2-D matrices vertexes *
> time_frames). Is there a tool that can do this easily, or do you have
> other recommendations how to do this?
>
> Thank you!
>
>
>
>
> _______________________________________________
> 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
greve@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: 7
Date: Mon, 4 Dec 2017 12:50:20 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] QDEC and comparing two conditions
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <e9ec8a98-c015-0050-9ede-fa91008f215c@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=windows-1252; format=flowed
If you want to do a conjunction, you can run mri_concat with the
--conjunct option (see --help for more details). If you want to look at
simple overlap, you can threshold each sig map (mri_binarize), then
combine them together something like
fscalc map2.bin.nii.gz mul 2 add map1.bin.nii.gz -o overlap.nii.gz
overlap will be
1 for map1 only
2 for map2 only
3 for both
On 11/30/2017 01:46 PM, Rizvi, Batool wrote:
>
> Hi ? I?m still wondering what would be the best method to perform the
> mentioned steps. Additionally, would mri_compute_overlap provide
> output related to spatial overlap and difference, that we?re looking
> for? Is it possible to do this with thickness, or maybe not ? because
> it doesn?t consider area? Just wondering, as we only performed QDEC
> using thickness so far.
>
> Thanks so much,
>
> Batool
>
> *From:* Rizvi, Batool
> *Sent:* Tuesday, November 28, 2017 3:16 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* QDEC and comparing two conditions
>
> Hi FreeSurfer experts,
>
> We calculated the correlation between thickness two different
> behavioral conditions using QDEC. We now want to compare the spatial
> overlap and difference in thickness-correlation between the two
> behavioral conditions. We would like to do this both visually as well
> as statistically. Is there an option to do this either in QDEC or in
> the command line?
>
> Thanks for your time!
>
> Batool
>
>
>
> _______________________________________________
> 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
greve@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: 8
Date: Mon, 4 Dec 2017 12:57:18 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Combining parcellated regions within an
atlas?
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <ab6331c8-0280-b9e4-df9f-456c0285439f@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=utf-8; format=flowed
You can break the annotation into separate labels
(mri_annotation2label), then merge the ones you want into a single label
(mri_mergelabels), then recombine them into an annotation (mris_label2annot)
On 11/29/2017 10:03 PM, Michiko H. wrote:
> Hi Freesurfer Experts,
>
> I was wondering what the best way of combining regions within a
> parcellation? For example, in the Schaefer 2017 functional atlas,
> there are regions such as:
>
> 7Networks_LH_DorsAttn_FEF_1 ? ? ? ? ? 0 118 22 ?0
> 7Networks_LH_DorsAttn_FEF_2 ? ? ? ? ? 0 119 17 ?0
> 7Networks_LH_DorsAttn_FEF_3 ? ? ? ? ? 0 119 18 ?0
> 7Networks_LH_DorsAttn_FEF_4 ? ? ? ? ? 0 119 19 ?0
> 7Networks_LH_DorsAttn_PrCv_1 ? ? ? ? ?0 119 20 ?0
> 7Networks_LH_DorsAttn_PrCv_2 ? ? ? ? ?0 119 21 ?0
>
> If I would like to combine all the DorsAttn_FEF areas into 1 node and
> DorsAttn_PRCv areas into another, what is the best way to do this? I
> currently have an image that has been parcellated using this atlas
> that was brought into volumetric space. I would need to have a
> transformed re-parcellated file and a corresponding color LUT file.
>
> Would appreciate any help, thank you!
>
> Best,
> Michiko
>
>
> _______________________________________________
> 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
greve@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
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------------------------------
Message: 9
Date: Mon, 4 Dec 2017 12:59:10 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Overlaying multiple results onto one surface
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <98c037e5-25b1-18f7-1325-5f9dac45c652@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=windows-1252; format=flowed
I think you would need to figure out what such a combination would look?
like. Eg, you could have a separate label for each possible combination
contrasts above threshold, though this would create a combinatorial
explosion.
On 11/29/2017 02:48 PM, Nguyen, Tin wrote:
>
> Hello,
>
> I have been running different analyses through QDEC GUI for different
> covariates that describe a similar construct, for instance:
>
> ?Model A: (cortical thickness) ~ (covariate 1) + (nuisance factors)
>
> ?Model B: (cortical thickness) ~ (covariate 2) + (nuisance factors)
>
> ?Model C: (cortical thickness) ~ (covariate 3) + (nuisance factors)
>
> ?Model D: (cortical thickness) ~ (covariate 4) + (nuisance factors)
>
> ?Model E: (cortical thickness) ~ (covariate 5) + (nuisance factors)
>
> As a result, I have 5 different brain images to illustrate each of the
> 5 models for their corresponding covariates. Is there way to overlay
> all 5 of the images onto a common space to have 1 representative brain
> image? This is to show overlapping effects, or the lack thereof, of
> the covariates.
>
> Thank you.
>
> -Tin
>
>
>
> _______________________________________________
> 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
greve@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: 10
Date: Mon, 4 Dec 2017 14:17:39 -0500
From: Nicole Orme <nicoleaorme@gmail.com>
Subject: [Freesurfer] recon edit error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <8378B2B8-EB83-4C7D-8A54-E3ED470DC7A3@gmail.com >
Content-Type: text/plain; charset="utf-8"
Hello FreeSurfer Developers,
I have been editing my MRI images using the recon edit tool. I have been editing the white matter so it does not include grey matter. When I click shift to remove the extra voxels included in white matter they are removed, which is what supposed to happen. Where I?m encountering a problem is sometimes I?ll have clicked the shift but are not holding the mouse down so it seems as if the entire image gets selected. I?ve attached a screenshot. I don?t know how to reverse this. It then will have all the images selected.
If you could help me that would be great!
Nicole
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