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, freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:
- Re: mri_binarize (Douglas N Greve)
- Re: Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess (Douglas N Greve)
- Re: freesurfer design (Douglas N Greve)
- Re: subcortical structures volume (Douglas N Greve)
- Re: mri_vol2surf wrong hemisphere (Douglas N Greve)
- Re: Concatenating .mgh surface space functional MRI runs (Douglas N Greve)
- Re: QDEC and comparing two conditions (Douglas N Greve)
- Re: Combining parcellated regions within an atlas? (Douglas N Greve)
- Re: Overlaying multiple results onto one surface (Douglas N Greve)
- 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
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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:
- 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
- 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
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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
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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
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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
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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!
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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
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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
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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
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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. Ihave 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