[Freesurfer] Average intensity from functional image within a label along the surface

[Erik Jahner]

External Email - Use Caution

 I am interested in obtaining the average intensity within a label from each 
frame of a functional image that has been smoothed on the surface  (I have 
generated the label). However, the functional connectivity pipeline seems to 
use only volume based seeds. It seems to me that in using the FreeSurfer 
software we would want to take advantage of the surface based smoothing and not 
return to getting the average of voxels in aparc+aseg. 

(1) Am I incorrect in my thinking here?

(2) Is there a way to get the mean intensity of a label (I have created) at 
each frame along the surface to get a timcourse for a particular region?

I see there is a way to do this with anatomical features such as thickness, but 
I do not see a way to do this with functional data across frames for signal 
intensity. 

Thanks
~Erik Jahner




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

Re: [Freesurfer] question about longitudinal data analyses

[Douglas N. Greve]

On 7/9/2021 11:44 AM, Ritobrato Datta wrote:


External Email - Use Caution

Hi All,


I have the following data –

I have 205 subjects - each subject was imaged at 3 timepoints 
(baseline, followup 1 and followup 2)


The 205 subjects are split in two treatment arms with 100 subjects in 
the first one and 105 subjects in the second one.


For each timepoint, I have created FA maps in their native diffusion 
space.


I have also extracted the mean FA maps for 187 ROIs using mri_segstats.

For each timepoint, I have saved the results as a matrix (FA in 187 
ROIs x 205 subjects) in a text file.


So I have three files for the three timepoints.

I have the age and cognitive score for each subject at each timepoint. 
And their gender.


I want to answer the following questions –

 1. Do the baseline FA correlate with the corresponding cognitive
score at baseline ?

This is a straight forward group analysis, so see 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples (maybe the Two 
Groups (1 Factor, Two Levels), One Covariate 
)


 1. I am interested in testing whether the FA changed significantly
across the different timepoints and does that relate to the change
in the cognitive score


See https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova


 1. Is there an effect of treatment on this change in FA across time ?


Also see https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova


Can you please suggest what programs in freesurfer will allow me to 
test these questions on both voxelwise and ROI wise ?



Many thanks for your help and guidance,


Regards


Rito


___
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
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] LGI FS 7.1

[Del Re, Elisabetta]

External Email - Use Caution

Would you normalize for differences in head size by adjusting for eTiV or total 
surface area?
Thank you so much,
Elisabetta

Sent from my iPhone

On Jul 9, 2021, at 2:08 PM, Douglas N. Greve  wrote:

 I'm not sure what you mean. Can you elaborate?

On 6/30/2021 5:05 PM, Del Re, Elisabetta wrote:

External Email - Use Caution

External Email - Use Caution

Thank you so much.
I am still in doubt as to whether adjust/normalize for brain volume or 
otherwise surface area before comparing groups.
Thank you for your advise,
best wishes,
Elisabetta

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Sunday, June 20, 2021 10:34 AM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] LGI FS 7.1

The biggest changes are intensity normalization and highres support, but many 
more changes. See the release notes
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1Di65Y_P78CLycNjcfkSgtF_4x3lfpFYC8zd_H_tKCcJRA64q2OhpxFq3TyW_zgV0gMdDuzMVAMK6TCpfsDQG3x0jkrxDDGAi90f2R7NYsQt1bRa4ujKr2hgla9oI0C4TulpP1VXJxSw7l6bW8__ycil-Jp2zeq3FdGK262uP3sYu7yxufq7pivevw_u6cuEHiaH_fkdTbsUj8S3cJ25pOSDwnGEEwP6WLSBSytBkn-Z_mbRwGikkYUo1KG8F6c_iqEh2Mt6e4G69MR8zABKJRw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes


On 6/9/2021 10:17 AM, Del Re, Elisabetta wrote:

External Email - Use Caution

External Email - Use Caution

Dear FS team,
what are differences if any between LGI in FS 5.3 and 7.1?
Thank you so much,
best wishes,
Elisabetta



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1sLeUzUQ901lGnNjwPD2kwN8sTPX4PBy7pYeeGHSUcTGTpyPQVYe6iXhPFScxxTKPHCSwO_YuHw6MKNJGzgJtS8uEnX2_kvT_nS9W1TOItISbcDoX29GssQprhBVXb9Cs5WdVi3awt3zBuAJ_gRYP4MwqTriJGGx9WOsGmUvc76DqpyhV4KQNFD3srHa6uD7lW3hKBSgSJiJLglZTpqqVChh9eSz28PfY9xhZTv4bkkSxY8nPaqL7gZzD9sbN1IrCNI3hQgR73dSx9UJA48RxEg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer




_

Re: [Freesurfer] Freesurfer longitudinal stream error

[Douglas N. Greve]

Try running it without the -parallel flag. If you want to use multiple 
cores, then add -threads N (N= number of cores)


On 7/6/2021 4:29 AM, Susanne Gellißen wrote:

    External Email - Use Caution

Dear FreeSurfer Developers,
I am processing MRI data using the freesurfer processing stream with 
two timepoints. I already executed the individual 
freesurfer-processing for each subject and timepoint and also the 
recon-all -base step. All finished without errors.
When running the recon-all -long command, the processing stream exits 
at the same step in the script for all subjects and timepoints. I 
cannot identify a particular error message (ony at the end the script 
says exited with errors and no stats files are produced).

 I am using freesurfer 7.1.1 on an iMAc with macOS Catalina.
Please find attached the recon-all log files for the longitudinal 
streams (2 folders with “long” in the foldername) as well as for the 
preparation steps.



Thank you.




---

PD Dr. med. Susanne Gellißen

Department of Diagnostic and Interventional Neuroradiology
University Medical Center Hamburg-Eppendorf
Martinistraße 52, 20246 Hamburg
E-mail: s.siemon...@uke.de



--

_

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen 
Rechts; Gerichtsstand: Hamburg | 
http://secure-web.cisco.com/1HvVVbdMRr6qAu-L5y0c3HUFOZFKnzwzd2mFmsc4xoj1PMvHBZwQvrGMpUgr9mfBpN5hjM2R9dTml5iZZwEVwt-nEs4X5Z7IMAiBjsdv05MYZShXijGytKC09fYoZNsuKkkeCWhAZFMDOzCIyzaPUqFtCIzEWdphDQC89YcffIRfKfjMomVcKnc0J1ACVq4R4QeNFoo1P_nAX6nwpuILDzsXgN5-9GPacTKJvBBEAE9fEQ43-90fE5pf1DXRrMvh2hGS5qwFSjGaBGDs0vRV5vyNSYQm9l2KixSaD6hRT9ag/http%3A%2F%2Fwww.uke.de 

Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim 
Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel

_

SAVE PAPER - THINK BEFORE PRINTING
___
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
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Visualizing specific cortical parcels in Desikan Killiany atlas

[Douglas N. Greve]

In FreeView, go to "View/Edit". From the resulting interface, you can 
turn on and off any parcellations you want.

On 7/5/2021 1:04 PM, Ellen Ji wrote:
>  External Email - Use Caution
>
> Dear experts,
>
> I have a basic visualization question.
> I would like to create a surface brain figure with specific cortical
> parcels colored. Similar to
> https://secure-web.cisco.com/1DryTPj2WrD-LULa8TF6HVh2xwKTLAaWDFvIpAUrs4z6O2VOFttAjezDQX2aR4Z5m6bFRIWk8l6q3Kc0B4K1EjsGa3Ps7AUkb5SPODPx-r-FwnmCtHYHHKbdbpiaWUNhY_vlBvQaG-4Cl9kGxomgOLjtwUjpfxAwjLULtd8raS9pKKnnCsUkx0wW3RSuyX62NEemue5GJ8QZ5J46l4PfzCFjifys8EQeNVKxstOck3xiE-BXhju-kVWs7GQxLXjjk6zMrtaHPswi0sl3CPcqM2A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview%3Faction%3DAttachFile%26do%3Dget%26target%3Dgood_output_aparc_crop.png
> but not with ALL parcels in the atlas selected.
>
> I know that I can go into a subject folder and load this freeview -f
> surf/lh.pial:annot=aparc.annot in order to see the entire Desikan
> Killiany atlas. However, I would like to select 4-5 rois.
>
> What's the best way to do this? It won't be related to any results and
> doesn't need to be from a particular subject's brain (can also be
> fsaverage). It's purely to highlight some cortical parcels for
> visualisation purposes.
>
> Thanks,
> Ellen
>
> ___
> 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
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Transformation Applied to T1.mgz during recon-all

[Douglas N. Greve]

We refer to this operation as "conforming".
This page might help
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

On 7/4/2021 4:39 PM, Alexander Rockhill wrote:
 > External Email - Use Caution
 >
> Hello,
>
>    I am trying to replicate the processing steps that occur between 
> when a T1 is given as input to recon-all and the T1.mgz that is stored 
> in the $SUBJECTS_DIR/$SUBJECT/mri directory for mne-bids and dealing 
> with mne's internal dependency on the surface RAS coordinate frame.
>
>    It is my impression that 1) the image is resampled to 256 x 256 x 
> 256 and then 2) the image is reoriented to head-first supine aka LIA 
> aka scanner space. But when I replicate these steps using nibabel, the 
> affine is off by a rotation and translation:
>
> T1.mgz
> --
>
>   [[ -1.    ,  -0.0015,  -0.0003, 132.77600098],
>    [  0.0003,   0.0001,   1.    , -94.00223541],
>    [ -0.0002,  -1.0012,  -0.0001, 149.55487061],
>    [  0.    ,   0.    ,   0.    ,   1.    ]]
>
> orig resampled and translated
> -
>
>   [[ -0.5208,  -0.00905184,   0.00373623, 164.44344257],
>    [  0.00337327,   0.03978604,   0.99920255, -98.49012464],
>    [  0.00919327,  -0.9991672 ,   0.03975359, 141.93864847],
>    [  0.    ,   0.    ,   0.    ,   1.    ]]
>
> orig to T1.mgz transform affine
> ---
>
>   [[  0.5203,  -0.00337331,  -0.00919312, -30.68693093],
>    [  0.0037362 ,   0.99920251,   0.03975359,  -1.8476189 ],
>    [  0.00905186,  -0.03978605,   0.99916736,   2.32735433],
>    [  0.    ,   0.    ,   0.    ,   1.    ]]
>
> Since there are off-diagonal entries in the last affine, I assume 
> there is some kind of rotation, and since there are non-zero entries 
> in the last column, I assume there is some kind of translation as 
> well. I am not sure what either of those would be from so any advice 
> or help would be appreciated.
>
> Alex Rockhill
> PhD Candidate University of Oregon
>
 >
 > ___
 > 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
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] setwdelay error 1 weight

[Douglas N. Greve]

By my count, you entered 36 weights. I'm not sure why it says you only 
entered 1, but try the correct number of weights first and see if the 
problem goes away


On 7/3/2021 2:08 PM, Marilena Wilding wrote:


External Email - Use Caution

External Email - Use Caution

Dear Freesurfers,

for my FIR model I’d like to use the -setwdelay option in the 
mkcontrast-sess command.


My command looks like this:

mkcontrast-sess \

-analysis FIR_group_20-lh -contrast global-v-local \

-a 2 -c 1\

-setwdelay

When I run this the promt appears for the delay weights. But when I 
enter them, I always get an error:



mkcontrast-sess -analysis FIR_group_20.lh -contrast global-v-local -a 
2 -c 1 -setwdelay


INFO: Found 2 Non-Null Conditions
INFO: Found 29 Delays
Condition Weights: -1. 1.
###
### Enter 29 Delay Weights (Return)
1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ERROR: entered 1 weights, needed 29


I'm entering 29 values (I want to include only the first seven TPs) 
but apparently only 1 value is detected.


Could you please help me? I'm really out of ideas here.


Thanks a lot in advance!


Marilena


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1Yt-6vFp02urjaFdPDprwvlGtXOc-N8qmUiTZzLfBOjUncdtPkMQc_pGuybq2uKL-F9P5o1u4y5OHtMx1dqOqVUfWkOgHHB74Gy_Eo0Hz1ZsKZwkpcXkqV7YnMrE4ZjdtzqvvaeM6lYsWU7_wgEapxoTFv-gfdu3y6fw4Cy3cpi60Vkb8_cX72fk0qT8vawhZ8lHM3-VqcIUIWnU30nf_NwsN0oJ9q3Jp_hGSSL9b40AWzytz8zVOkTyn1l5_ElHAMZAbkULg5rN160HU2O4Jeg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer


___
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] What is the relationship between qdec results and aparc.stats?

[Douglas N. Greve]

ROI-wise and vertex-wise analyses are different and may give different 
results. The vertex-wise analysis looks at individual vertices whereas 
ROI-wise averages over all the vertices. It is possible (even expected) 
that averaging over all vertices will reduce the variation and give 
stronger statistics than vertex-wise.

On 7/2/2021 10:07 AM, Satoko KINA wrote:
>  External Email - Use Caution
>
> Hello Freesurfer Developers,
>
>
> As a result of whole-brain analysis using qdec, specific regions with 
> significant differences between the two groups were depicted (e.g., 
> paracentral cortical thickness).
> Based on this result, we compared the paracentral region on the 
> Desikan-killiany atlas from aparc.stats between the two groups, and found 
> significant differences not only in CT but also in items rejected by qdec 
> (e.g., curv). How should we interpret this result? Which result is more 
> reliable? Can we consider the result of the analysis focused on a narrow 
> region of each ROI as a more detailed result because qdec is a whole brain 
> analysis?
> I am not familiar with statistics, so please forgive me if this is a 
> misguided question.
>
> Thank you for help!
>   
>
> Satoko
>
> ___
> 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
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Hippocampal Subfield Definition Errors

[Iglesias Gonzalez, Juan E.]

Dear Franchesca,
Could you please attach some images illustrating the problem?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

On Jul 9, 2021, at 13:06, Franchesca Kuhney 
mailto:fkuh...@uic.edu>> wrote:


External Email - Use Caution

Hello,

I've run into an issue with the longitudinal hippocampus/amygdala segmentation 
(segmentHA_T1_long.sh). All of the commands ran properly and I got the outputs 
listed on the FreeSurfer wiki but, upon QAing the segmentations, I realized 
that a few subjects hippocampal segmentations were a poor fit. It appears that 
the segmentation includes their parahippocampal gyrus. I'm wondering if you 
have any recommendations for how to fix these either manually or automatically? 
Thank you!

Kindly,
Franchesca

Franchesca Kuhney, M.A. (she/her)
Clinical Psychology Doctoral Student
University of Illinois at Chicago
Behavioral Sciences Building | Rm 3019
1007 W. Harrison St. | Chicago, IL 60607
[https://secure-web.cisco.com/1puxmEK3mDm56IT5JV-3zOLSqMv5RYqFgYmoHYrQAp5MYBlH0FXgFmM2N6W2VgtUPqMnfqlwxhCUv48gthl3zpOFiFLDXBi-4UJn9X_iohYJ1MZ77rnkRSf-6io9SHkp51H6LTDgc9AVbUnDsOaOpjELnIyceWsALuSm9SvfwsWWxk2Fgy5XW_lQaQWtUnrvFhp5lGHL-Us4-ypqNv2jHbdT6cj1v1zyi-_8nePwm054SFDv4xbrcB67amiyHtbWyZra43v0abbt1OA_yPlZbbQ/https%3A%2F%2Fdrive.google.com%2Fa%2Fuic.edu%2Fuc%3Fid%3D1R1NXIxIFqUxTPkk1dgc36H1tbzYr63aH%26export%3Ddownload]
-
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues.
The information included in the email may be confidential and is meant only for 
the use of the intended recipient.
If you received this communication in error, please notify the sender 
immediately and destroy the original information.
___
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
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Edit pial surface

[Douglas N. Greve]

You can use the reposition surface tool in freeview. Just be careful 
that you don't overwrite it if you re-run


On 7/2/2021 3:37 AM, Rosalia Dacosta Aguayo wrote:


External Email - Use Caution

Dear Freesurfer's experts,

I wonder if there is any chance to correct the pial surface when it 
does not cover entirely certain regions of GM, such for example, 
orbital frontal cortex


Kind regards,
Rosie

*
*


___
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
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Question about Extracting QDEC Results

[Douglas N. Greve]

which results? sig maps (and other maps) are surface overlays. You can 
convert them to nifit format, but they will still be surface overlays 
(so you would not view/analyze them in FSL or SPM)


On 7/1/2021 9:12 PM, Sonya Gupta wrote:


External Email - Use Caution

Hi,
Hope you are having a wonderful evening!
I was wondering, is there a way to extract results from QDEC as a 
NIFTI file? If not, in what format can you the extract QDEC results?


Thank you!

Sincerely,
Sonya

___
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
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Help segmenting all subjects in a folder

[Douglas N. Greve]

That does not apply to the recon-all command, only to 
mri_segment_hypothalamus_subunits



On 7/1/2021 12:23 PM, g.ton...@libero.it wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

Thank you for your work !
I successfully set up Freesurfer and ran a test on my computer, and I 
am now attempting to run recon-all on all subjects in a folder 
("/home/users/s/saccaro/Groupe_0" in the example script below). I run 
the analysis on a HPC (SLURM system).


I found that, concerning the recon-all command, "If no name is given 
after --s, the code will be run on ALL subjects in $SUBJECTS_DIR 
." 
but I do not find information on how this could work also for the 
previous step, mri_convert: is there a way to submit a job to segment 
all subjects in the folder "Groupe_0", and not just S001 (in the 
example below)? All folders are structured as follows: 
/S@@@/scans/struct/@@.nii .


I am new to Freesurfer and I apologize if my question is naive but I 
cannot find a solution in any of the online resources.


Thank you very much for your time!
Best,

Giorgio

*- Script, without SBATCH settings (I join the full version):*

module load FreeSurfer/6.0.0-centos6_x86_64
source /home/users/s/saccaro/SetUpFreeSurfer.sh
FSDIR="/home/users/s/saccaro/Groupe_0"

mksubjdris ${FSDIR}/S001;

mri_convert -i 
${FSDIR}/S001/scans/struct/s44891-153636-1-00192-1.nii -o 
${FSDIR}/S001/scans/struct/s44891-153636-1-00192-1.mgz


recon-all -all -s S001

___
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
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] fcseed-config

[Douglas N. Greve]

you should not pass it a label. If you look at the help,
Functional ROI-based options
  -roi fcconfig : as created by funcroi-confg


On 7/1/2021 10:58 AM, Nasiriavanaki, Zahra wrote:

Hello Freesurferers,

I’m trying to use a functional label (extracted from task functional 
BOLD data), as a seed for functional connectivity.
I tried to use the fcseed-config with -roi , but when I ran the 
fcseed-sess, I got this error: “If: expression syntax error”.

Could you please let me know what the problem is?


fcseed-config  -roi ${label}.label  -fcname ${label}.dat -fsd rest 
-rlf restruns -mean -cfg ${label}.config -force


fcseed-sess  -s ${subj}   -d ../  -cfg /${label}.config

Thanks,
Mona


*Zahra (Mona) Nasiriavanaki, M.D.*
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Boston, MA, USA, 02129


___
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
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Can I extract GLM values?

[Douglas N. Greve]

There should be a file called something like gamma.table.dat
This is a text file with the differences for each ROI and contrast.

On 7/1/2021 4:39 AM, Thalhammer, Melissa wrote:


External Email - Use Caution

Dear FS experts,


I have run mris_preproc and mri_glmfit for group analysis as described 
in the docs. My current project deals with the analysis of cortical 
thickness of preterm- vs. term-born adults and I want to correlate the 
difference in cortical thickness between those two groups with gene 
expression data. Thus, I would need the group difference ROI-wise as 
values in a spreadsheet/text file to perform correlation lateron. I 
have used the following code with the --table flag and have used 
cortical thickness data extracted with aparcstats2table as input.


Is there a way to extract the ROI-wise group difference, corrected for 
the covariates included into my GLM model?



Best,

Melissa Thalhammer


___
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
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] LGI FS 7.1

[Douglas N. Greve]

I'm not sure what you mean. Can you elaborate?

On 6/30/2021 5:05 PM, Del Re, Elisabetta wrote:


External Email - Use Caution

External Email - Use Caution

Thank you so much.
I am still in doubt as to whether adjust/normalize for brain volume or 
otherwise surface area before comparing groups.

Thank you for your advise,
best wishes,
Elisabetta

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Sunday, June 20, 2021 10:34 AM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] LGI FS 7.1
The biggest changes are intensity normalization and highres support, 
but many more changes. See the release notes
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes 




On 6/9/2021 10:17 AM, Del Re, Elisabetta wrote:


External Email - Use Caution

External Email - Use Caution


Dear FS team,
what are differences if any between LGI in FS 5.3 and 7.1?
Thank you so much,
best wishes,
Elisabetta

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu  
https://secure-web.cisco.com/1sLeUzUQ901lGnNjwPD2kwN8sTPX4PBy7pYeeGHSUcTGTpyPQVYe6iXhPFScxxTKPHCSwO_YuHw6MKNJGzgJtS8uEnX2_kvT_nS9W1TOItISbcDoX29GssQprhBVXb9Cs5WdVi3awt3zBuAJ_gRYP4MwqTriJGGx9WOsGmUvc76DqpyhV4KQNFD3srHa6uD7lW3hKBSgSJiJLglZTpqqVChh9eSz28PfY9xhZTv4bkkSxY8nPaqL7gZzD9sbN1IrCNI3hQgR73dSx9UJA48RxEg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
  




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1vxZfNE8vKzlRbZ8-Br6JzchyoXMsqWPJ4KtFmMCRyz0H4s8GJtnuSDBYjqbuEafy40nKvHbZcoAc8umnPbQY4jJpwGNKOaZweZH4kfYE1BiHuTsEuVXTdvc5vVVaZeTGyqvRnmhopWTEJiEgRmd2WgSW7tLPY0tzC1CD8fBEhKTB9vowqyDMhyAJz9kjGJsq7dCbBWCdryJmmDOQf_ZfKKdSycfwiws_lPv7jgbogaRXLAPdZ8NUfv3vRozLHyV1CAM3uyq5jIVug0lbL6b2wQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer


___
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] mri_glmfit DOSS

[Douglas N. Greve]

You cannot use a DODS in this design as it tries to fit an offset and a 
slope for each class, which can't be done when the class has only one 
member. Try using DOSS instead. You should probably demean and rescale 
the eTIV to be between 0 and 1.


On 6/29/2021 11:19 AM, Dr. Cornelius Kronlage wrote:


External Email - Use Caution

Dear freesurfers,

for a morphometry study, I am comparing a single subject at a time to 
a group of controls. I would like to include age, gender (as a 
continuous variable for the sake of simplicity) and eTIV as “nuisance” 
regressors in the GLM. The FSGD looks like this:


GroupDescriptorFile 1
    Title SUBJECT1_vs_allControls
    Class Test
    Class Controls
    Variables Age Gender eTIV

Input SUBJECT1 Test 50 1 1497422.2500
Input SUBJECT2 Controls 30 0 1709039.536815
Input SUBJECT3 Controls 29 0 1423097.816203
Input SUBJECT4 Controls 31 1 1524690.026713
...

When I try to run mri_glmfit I get the following error even though I 
specify DOSS:


$ mri_glmfit --fsgd SUBJECT1_vs_allControls.fsgd doss [...]

gdfRead(): reading SUBJECT1_vs_allControls.fsgd
WARNING: variable 1 is "Gender" which is often a discrete factor
  The proper way to handle discrete factors is to create classes.
  See https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 28.6875 6.36611
1 Gender 0.46875 0.499022
2 eTIV 1.51444e+06 125811
Class Size and Means of each Continuous Variable
1 Test  1  50.   1. 1497422.2500
2 Controls 31  28.   0.4516 1514993.8589
ERROR: Class Test has 1 members. With 3 variables and using DODS, you 
need at least 4 members


How do I get mri_glmfit to use DOSS, or do I have to specify the 
design matrix by hand in this case?


Thank you!

Best wishes
Cornelius


___
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
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all soft errors

[Douglas N. Greve]

On 6/29/2021 3:32 AM, Rosalia Dacosta Aguayo wrote:


External Email - Use Caution

Dear Freesurfer team,

I am inspecting the different participants I have run recon-all -all 
and I have found different errors I would like to discuss with you 
before proceeding as I am new with this software.


1. I have found dura at some regions of the brain. I should use gcut 
or delete voxels?

I've never used gcut, but deleting voxels will work
2. I have found discontinuity in GM and what I should do with this 
(attached photo 2)
Not sure what you are pointing to. Some of the problems may be in the 
medial wall (which is not a problem).
3. In photo 1, not sure at some regions were to consider wm as it is 
not clear for me...any suggestion with this one? I think it should be 
done with cp, right?

I guess so. The data quality looks pretty low, so it might be hard to tell.


Kind regards,
Rosie

*
*


___
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
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Problem with mri_glmfit-sim

[Douglas N. Greve]

I think this might be a bug. You might be able to get around it by 
adding --no-perm-resid as the last option. Why are you running your own 
simulation instead of using the precomputed tables?


On 6/28/2021 1:38 AM, juergen.haen...@upd.unibe.ch wrote:


External Email - Use Caution

Dear Douglas

please find the terminal output and the log files attached.
when I run this command in FS 6.0.0, no error occurred

thanks in advance

cheers
Jürgen



Am 27.06.2021 um 16:49 schrieb Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>:


Can you send the mri_glmfit.log file from your mri_glmfit run?
Can you run mri_glmfit-sim with --debug as the first option and 
capture and send the output?


On 6/23/2021 4:42 AM, juergen.haen...@upd.unibe.ch 
 wrote:


External Email - Use Caution

Dear FS experts

I have run stats using mri_glmfit (FS 7.1.1 on Mac) with the 
following command


mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd 
IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH.glmdir 
--surf fsaverage lh --C IPS_2groups.mat --cortex


and everything worked fine. When trying to run simulations with 
mri_glmfit-sim with the following command


mri_glmfit-sim --glmdir IPS_2groups_n135_Thickness_LH.glmdir --sim 
mc-z 500 1.302 lh_mc-z.abs_500p1.3 --sim-sign abs --overwrite 
--cwpvalthresh 0.25


the following error occurred

Loading y from 
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
error: mri_read(): couldn't determine type of file 
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force

... done reading.
ERROR: loading y 
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force


The entire output is shown below.
I do not understand why after the —y option in the command reported 
by FS in the terminal, i.e.


mri_glmfit --C 
IPS_2groups_n135_Thickness_LH.glmdir/tmp.mri_glmfit-sim-96372/IPS_2groups.mtx 
--sim mc-z 500 1.302 
IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001 
--sim-sign abs --fwhm 14.598750 --fsgd 
IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd dods --mask 
IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh --y --perm-force 
--surf fsaverage lh white


the input file (IPS_2groups_n135_lh_thickness.10.mgh) is missed and 
hence the following option —perm-force is interpreted as input file.


How can I fix this problem?

Thanks in advance for any advise
Regards
Jürgen


---
entire output:

[upddkp224:average_IPS_FS7_Linux/stats/glm_group_n135] jurgenhanggi% 
mri_glmfit-sim --glmdir IPS_2groups_n135_Thickness_LH.glmdir --sim 
mc-z 500 1.302 lh_mc-z.abs_500p1.3 --sim-sign abs --overwrite 
--cwpvalthresh 0.25
cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd 
IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH.glmdir 
--surf fsaverage lh --C IPS_2groups.mat --cortex

SURFACE: fsaverage lh
log file is 
IPS_2groups_n135_Thickness_LH.glmdir/lh_mc-z.abs_500p1.3.mri_glmfit-sim.log


cd 
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135

/Applications/freesurfer/bin/mri_glmfit-sim
--glmdir IPS_2groups_n135_Thickness_LH.glmdir --sim mc-z 500 1.302 
lh_mc-z.abs_500p1.3 --sim-sign abs --overwrite --cwpvalthresh 0.25


FreeSurferEnv.csh 7.1.1
Wed Jun 23 10:19:19 CEST 2021
Darwin upddkp224.unibe.ch 
 
19.6.0 Darwin Kernel Version 19.6.0: Thu May  6 00:48:39 PDT 2021; 
root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64

jurgenhanggi
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd 
IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH.glmdir 
--surf fsaverage lh --C IPS_2groups.mat --cortex


DoSim = 1
UseCache = 0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 14.598750
nSimPerJob = 500
1/1 Wed Jun 23 10:19:19 CEST 2021
mri_glmfit --C 
IPS_2groups_n135_Thickness_LH.glmdir/tmp.mri_glmfit-sim-96372/IPS_2groups.mtx 
--sim mc-z 500 1.302 
IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001 
--sim-sign abs --fwhm 14.598750 --fsgd 
IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd dods --mask 
IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh --y --perm-force 
--surf fsaverage lh white

INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR
INFO: ignoring tag SynthSeed
simbase 
IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001

FWHM = 14.598750
gdfRead(): reading IPS_2groups_n135_Thickness_LH.glm

[Freesurfer] Hippocampal Subfield Definition Errors

[Franchesca Kuhney]

External Email - Use Caution

Hello,

I've run into an issue with the longitudinal hippocampus/amygdala
segmentation (segmentHA_T1_long.sh). All of the commands ran properly and I
got the outputs listed on the FreeSurfer wiki but, upon QAing the
segmentations, I realized that a few subjects hippocampal segmentations were
a poor fit. It appears that the segmentation includes their parahippocampal
gyrus. I'm wondering if you have any recommendations for how to fix these
either manually or automatically? Thank you!

Kindly,
Franchesca

*Franchesca Kuhney, M.A.* *(she/her)*
Clinical Psychology Doctoral Student
University of Illinois at Chicago
Behavioral Sciences Building | Rm 3019
1007 W. Harrison St. | Chicago, IL 60607

-
*Electronic Mail is not secure, may not be read every day, and should not
be used for urgent or sensitive issues.*
*The information included in the email may be confidential and is meant
only for the use of the intended recipient.*
*If you received this communication in error, please notify the sender
immediately and destroy the original information.*
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] smoothing volume data extracted using aparcstats2table

[Douglas N. Greve]

Generally, you do not smooth it as averaging over the ROI is effectively 
a type of smoothing. If you were to smooth prior to the averaging, you'd 
get one area smearing into another.


On 6/28/2021 12:57 PM, Ryan Bell, Ph.D. wrote:


External Email - Use Caution

Dear Freesurfer Experts,

I am wondering whether the extracted ROI volume data acquired when 
using the command aparcstats2table needs to be smoothed?  I performed 
surface smoothing using surf2surf for cortical thickness data, but 
cannot find a way to smooth the volume data listed in 
aparcstats2table.  Is it recommended that I do not perform smoothing?


Thank You,

Ryan

---

Ryan Patrick Bell, Ph.D.
Research Analyst, Department of Psychiatry & Behavioral Sciences
905 W. Main St., Suite 24-E

Durham, NC 27701

Phone: (919) 681-3495

Email: ryan.b...@duke.edu 

Website: _*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* http://sites.duke.edu/harp/ 
_


Twitter: *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* twitter.com/HARPatDuke 
 




___
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
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Calculating group-wise Dice Similarity Coefficient and corresponding surface map

[Douglas N. Greve]

try $FREESURFER_HOME//matlab/annotval2surfoverlay.m


On 6/25/2021 2:55 PM, Fischl, Bruce wrote:


I guess doing it in matlab would be easiest

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Hye Min Shin

*Sent:* Friday, June 25, 2021 1:24 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Calculating group-wise Dice Similarity 
Coefficient and corresponding surface map


*External Email - Use Caution *

Thank you for the response Bruce.

I apologize for the confusion regarding surface map but what I was 
trying is that I wanted to create a surface file that contains dice 
coefficients for labels across the entire cortex. With your response, 
I think I can get the average dice coefficient for each label and 
hopefully create a surface map that visualizes dice coefficients on 
brain surface map.


Would there be a way to create my own surface map with brain 
morphometry values that I created?


Best,

Julia Shin


___
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
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Cortical thicknees normalization values

[Douglas N. Greve]

We generally do not normalize it by anything. ICV norm is not needed 
because thickness does not scale with head size. Sometimes people will 
normalize by mean thickness, but that changes the question being 
answered, so that is more a question for you


On 6/24/2021 3:01 PM, Gabbo Ramírez García wrote:


External Email - Use Caution

External Email - Use Caution



Hi freesurfer user.

I have been working with some cortical thickness values of a control 
group to test some changes related to cognitive training. However, I 
have been hesitating about whether I have to normalize the cortical 
thickness values (as happens with subcortical volumes and ICV) or not. 
I have read a little about it and I understood that I could use the 
ICV or/and mean cortical thickness, but I didn't find a specific 
criteria to do or not this normalization. Any clue, recommendation, 
explanation or paper about this will be very helpful.


Thanks in advance.

*or reposting discussion of this question.

*Gabriel R.*



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1igRZreQyL28dpaDxcw1KUE3935aWbqlbZ8jIEL5JY7FolB-S-U_VYuvhI-5Zwj73nhgC-yUMsLNFXTFluiVPuSmaVXN_39-Fl9swxgpdrugnmgZcWEuaY_c1_qlT5n3npwt0ZxzDLdwQc_N9TsJzhh5fadopoPF69JY4lq0wrk290GbNgpWaY7WJ4J6b0HlMvdElGoKaR00AvVT9lr8sw_rI8ai-ICPblB-ChOhYFBVpX9kSY0-vkAa3uDoxaGaLdLPiZ4xv8LBhPTVAtlxy7Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer


___
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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] question about longitudinal data analyses

[Ritobrato Datta]

External Email - Use Caution

Hi All,


I have the following data –



I have 205 subjects - each subject was imaged at 3 timepoints (baseline,
followup 1 and followup 2)

The 205 subjects are split in two treatment arms with 100 subjects in the
first one and 105 subjects in the second one.



For each timepoint, I have created FA maps in their native diffusion space.

I have also extracted the mean FA maps for 187 ROIs using mri_segstats.

For each timepoint, I have saved the results as a matrix (FA in 187 ROIs x
205 subjects) in a text file.

So I have three files for the three timepoints.



I have the age and cognitive score for each subject at each timepoint. And
their gender.



I want to answer the following questions –



   1. Do the baseline FA correlate with the corresponding cognitive score
   at baseline ?
   2. I am interested in testing whether the FA changed significantly
   across the different timepoints and does that relate to the change in the
   cognitive score
   3. Is there an effect of treatment on this change in FA across time ?



Can you please suggest what programs in freesurfer will allow me to test
these questions on both voxelwise and ROI wise ?


Many thanks for your help and guidance,


Regards


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

[Freesurfer] Tracula 7.1.1 - trac-all - stat

[Fanny Noury]

   External Email - Use Caution


Hello FreeSurfer Developers,

I am just started to use "the trac-all -stat" command of Tracula 7.1.1 to 
reconstruct a mean tract for each pathway for all the subjects of a
group. Several files are created for each pathway in the "stat" directory.

What are the differences between these two files created for the AF, MD
AD and RD diffusion parameters :

- TRACTNAME_PP.avg33_mni_bbr.**.txt

- TRACTNAME_PP.avg33_mni_bbr.**_Avg.txt


Thank You very much for your help.


Best Regards,
F. Noury


-
Fanny NOURY, Ph.D
Associate Pr.
Rennes 1 University

LTSI UMR INSERM 1099
Université de Rennes 1
Campus Villejean - RDC Bât. 5
CS 34317
35043 Rennes Cedex
France


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