[Freesurfer] impact of defacing on eICV calculations

[Ritobrato Datta]

External Email - Use Caution

Hi All,

I have inherited some T1 data that are defaced.

If I run the defaced images through freesurfer, will that impact the eICV
calculations ?

Please let me know.

Many thanks

Ri
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[Freesurfer] error running samseg on cluster

[Ritobrato Datta]

External Email - Use Caution

Hi All,

I am trying to run samseg as follows on a cluster and am getting a message
that I need to install tensorflow (which is already installed). Please see
below.
Please advise how to fix this.

Many thanks

Rito
-
run_samseg --input t12t2.nii.gz t2_brain.nii.gz --lesion
--lesion-mask-pattern 0 1 --save-posteriors --output t2_lesions
error: This tool requires tensorflow, but fspython does not ship with
tensorflow
by default. You (or a sys admin) can install the CPU version via:fspython
-m pip install tensorflow==1.13.1

fspython -m pip install tensorflow==1.13.1

Requirement already satisfied: tensorflow==1.13.1 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (1.13.1)
Requirement already satisfied: protobuf>=3.6.1 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
tensorflow==1.13.1) (3.17.3)
Requirement already satisfied: keras-applications>=1.0.6 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
tensorflow==1.13.1) (1.0.8)
Requirement already satisfied: absl-py>=0.1.6 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
tensorflow==1.13.1) (0.13.0)
Requirement already satisfied: six>=1.10.0 in
/home/rito/software/freesurfer7/python/packages (from tensorflow==1.13.1)
(1.14.0)
Requirement already satisfied: grpcio>=1.8.6 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
tensorflow==1.13.1) (1.39.0)
Requirement already satisfied: termcolor>=1.1.0 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
tensorflow==1.13.1) (1.1.0)
Requirement already satisfied: astor>=0.6.0 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
tensorflow==1.13.1) (0.8.1)
Requirement already satisfied: gast>=0.2.0 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
tensorflow==1.13.1) (0.5.2)
Requirement already satisfied: numpy>=1.13.3 in
/home/rito/software/freesurfer7/python/packages (from tensorflow==1.13.1)
(1.18.4)
Requirement already satisfied: keras-preprocessing>=1.0.5 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
tensorflow==1.13.1) (1.1.2)
Requirement already satisfied: wheel>=0.26 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
tensorflow==1.13.1) (0.37.0)
Requirement already satisfied: tensorboard<1.14.0,>=1.13.0 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
tensorflow==1.13.1) (1.13.1)
Requirement already satisfied: tensorflow-estimator<1.14.0rc0,>=1.13.0 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
tensorflow==1.13.1) (1.13.0)
Requirement already satisfied: h5py in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
keras-applications>=1.0.6->tensorflow==1.13.1) (3.1.0)
Requirement already satisfied: markdown>=2.6.8 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (3.3.4)
Requirement already satisfied: werkzeug>=0.11.15 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (2.0.1)
Requirement already satisfied: mock>=2.0.0 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
tensorflow-estimator<1.14.0rc0,>=1.13.0->tensorflow==1.13.1) (4.0.3)
Requirement already satisfied: cached-property; python_version < "3.8" in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
h5py->keras-applications>=1.0.6->tensorflow==1.13.1) (1.5.2)
Requirement already satisfied: importlib-metadata; python_version < "3.8"
in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (4.6.3)
Requirement already satisfied: dataclasses; python_version < "3.7" in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
werkzeug>=0.11.15->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (0.8)
Requirement already satisfied: zipp>=0.5 in
/home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from
importlib-metadata; python_version <
"3.8"->markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1)
(3.5.0)
Requirement already satisfied: typing-extensions>=3.6.4; python_version <
"3.8" in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages
(from importlib-metadata; python_version <
"3.8"->markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1)
(3.10.0.0)
You are using pip version 18.1, however version 21.2.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
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Re: [Freesurfer] question about longitudinal data analyses

[Ritobrato Datta]

External Email - Use Caution

Good morning Doug,

I am trying to create a contrast matrix (also attached as a text file) for
the following conditions -

I have two treatment arms A and B
For treatment arm A, I have subjects 1, 2, 3 imaged at TP1, TP2, TP3
For treatment arm B, I have subjects 4, 5, 6 imaged at TP1, TP2, TP3.

I have used the repeated measures ANOVA tutorial to set up some of the
contrasts as follows -

GroupDescriptorFile 1
Title A-Vs-B-Long
Class A-TP1
Class B-TP1
Class A-TP2
Class B-TP2
Class A-TP3
Class B-TP3
Variables A-TP1-vs-A-TP2 A-TP1-vs-A-TP3 B-TP1-vs-B-TP2 B-TP1-vs-B-TP3
A-TP1-vs-B-TP1 A-TP2-vs-B-TP2 A-TP3-vs-B-TP3
Input sub1-TP1 A-TP1 1 1 0 0
Input sub2-TP1 A-TP1 1 1 0 0
Input sub3-TP1 A-TP1 1 1 0 0
Input sub4-TP1 B-TP1 0 0 1 1
Input sub5-TP1 B-TP1 0 0 1 1
Input sub6-TP1 B-TP1 0 0 1 1
Input sub1-TP2 A-TP2 -1 0 0 0
Input sub2-TP2 A-TP2 -1 0 0 0
Input sub3-TP2 A-TP2 -1 0 0 0
Input sub4-TP2 B-TP2 0 0 -1 0
Input sub5-TP2 B-TP2 0 0 -1 0
Input sub6-TP2 B-TP2 0 0 -1 0
Input sub1-TP3 A-TP3 0 -1 0 0
Input sub2-TP3 A-TP3 0 -1 0 0
Input sub3-TP3 A-TP3 0 -1 0 0
Input sub4-TP3 B-TP3 0 0 0 -1
Input sub5-TP3 B-TP3 0 0 0 -1
Input sub6-TP3 B-TP3 0 0 0 -1


Question 1 - My question is how do I setup the contrasts for the different
treatment arms -

A-TP1-vs-B-TP1 A-TP2-vs-B-TP2 A-TP3-vs-B-TP3

Question 2 - Also I have age and cognitive scores for each timepoint. How
do I add those to the contrast file ?

Thank you for the help,

Regards

Rito

On Mon, Jul 12, 2021 at 10:51 AM Douglas N. Greve 
wrote:

> Yes, it will work on both. If you use a table, then pass the table with
> --table tablefile instead of --y
>
> On 7/12/2021 7:54 AM, Ritobrato Datta wrote:
>
> External Email - Use Caution
> Good morning,
>
> Thanks Doug for the answers. Quick naive question. The analyses I want to
> perform are on volumetric data parcellated using aseg and not surface data.
>
> Does mri_glmfit work with the output of the asegstats2table or on
> voxelwise FA maps ?
>
> Many thanks
>
> Rito
>
> On Fri, Jul 9, 2021 at 4:04 PM Douglas N. Greve 
> wrote:
>
>>
>>
>> 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 *MailScanner has
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to
>> be* 
>> https://secure-web.cisco.com/1ZfuNLBplQ19J4Wa1OXL7_1Y-rjJvSIXBqjTAW29FzcfeaaeqYgi0u6AZHG4kchpYX7m8HUM6XmVdqjHa9z5fjgkoVWMMujW9D0JREjDnlQXxdpqo51YEvJar6CDUr32K2gt-FeJmb_hFjHreiACK0avb3oaIThmHLWgKEItcFeL_JI90lJdajfYMYESVaKlImLIEy6Mg1sn9-7c-BtkvhVRfKkdcL-VgQwsf9j_1VJzHr1Ii-tzV7Y5kxYlKl2PVJsQFWGHJoS2wb7RJSh0ChA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
>> <https://secure-web.cisco.com/1kTEkM43RMM06eViww_c18Pc-0P94xql3L2qK8iLarzzC3y3ZVsJIyVlzwF_FfFDswP_67I4PBLfYANWVTXuX-4X-dgKz6-k68o_AL_cvOJiFFFtpwIkd_pFO6m_tuaJtslVIIdmaO4umpQP9t8aMp-MPFEXKVDhKSsBgBNLINu7lLfDwLYKxiP2ZBbWcSlnNZ_KCTA3HDdKNI3PG_H6HTqTiwoC5vQjUicP6uxqYdn-HGl01ZnCt5V89LbOE3usywXIQtA_sZ4MgIcXGQDbj2g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples>
>>  (maybe
>> the Two Groups (1 Factor, Two Levels), One Covariate
>> <https://secure-web.cisco.com/1Rg-kxMT-3fQYeRaisunO8_YESB0oLHn151lBD4p9GXp_k96wsb_0fS3wm9AsXst9uQO9dbqRePqf6ijMZUnk_-eFE6HtBGPMjtgURPbRAk_5EC3Q0F3VX-mhUssaYthkDfBZtL6yv0bGjJhKRQulYDXsfvmbpUWl4VH11l7cdQD2p1m_QzCr5liecQPY6UPX6OiGxGITQdALxOE9JdoIyXv0aJ_ozwU_Lw9H2pA2lcXdQEb4RTfOartXbc2P58SNR1mmH4DIzvfp7MxOG1oqRA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdf2G1V>)
>>
>>
>>
>>1. I am interested in testing whether the FA changed significantly
&g

Re: [Freesurfer] question about longitudinal data analyses

[Ritobrato Datta]

External Email - Use Caution

Good morning,

Thanks Doug for the answers. Quick naive question. The analyses I want to
perform are on volumetric data parcellated using aseg and not surface data.

Does mri_glmfit work with the output of the asegstats2table or on voxelwise
FA maps ?

Many thanks

Rito

On Fri, Jul 9, 2021 at 4:04 PM Douglas N. Greve 
wrote:

>
>
> 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://secure-web.cisco.com/1kTEkM43RMM06eViww_c18Pc-0P94xql3L2qK8iLarzzC3y3ZVsJIyVlzwF_FfFDswP_67I4PBLfYANWVTXuX-4X-dgKz6-k68o_AL_cvOJiFFFtpwIkd_pFO6m_tuaJtslVIIdmaO4umpQP9t8aMp-MPFEXKVDhKSsBgBNLINu7lLfDwLYKxiP2ZBbWcSlnNZ_KCTA3HDdKNI3PG_H6HTqTiwoC5vQjUicP6uxqYdn-HGl01ZnCt5V89LbOE3usywXIQtA_sZ4MgIcXGQDbj2g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
>  (maybe the Two
> Groups (1 Factor, Two Levels), One Covariate
> <https://secure-web.cisco.com/1Rg-kxMT-3fQYeRaisunO8_YESB0oLHn151lBD4p9GXp_k96wsb_0fS3wm9AsXst9uQO9dbqRePqf6ijMZUnk_-eFE6HtBGPMjtgURPbRAk_5EC3Q0F3VX-mhUssaYthkDfBZtL6yv0bGjJhKRQulYDXsfvmbpUWl4VH11l7cdQD2p1m_QzCr5liecQPY6UPX6OiGxGITQdALxOE9JdoIyXv0aJ_ozwU_Lw9H2pA2lcXdQEb4RTfOartXbc2P58SNR1mmH4DIzvfp7MxOG1oqRA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdf2G1V>)
>
>
>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://secure-web.cisco.com/1l3pHvz1wZceoR8e52Wja_MsMNej9vi7VZZmS8c-z4MS9JGbI3TYJJMikCYf0s7kjh03rhGqRoz4Nqw5FjnWspM8jPaxx5vhTf6cgH1nVEw8kZAyGg-kIVm5tQNWqRiQ-S-cYslSRjWA5zKzXqqcgwKeSWShLW2aw-XRuSrV9IBOmdGQq2pERdmOAqXTVIKchIwtjPqefKoRqoYe4OZ6h_wlLLnBEFs_BJGv4A9Eabyq07igMiO8NeE8VYMkEhQFl0KlX_VyWmlAm-N28VS8hcg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova
>
>
>1. Is there an effect of treatment on this change in FA across time ?
>
> Also see 
> https://secure-web.cisco.com/1l3pHvz1wZceoR8e52Wja_MsMNej9vi7VZZmS8c-z4MS9JGbI3TYJJMikCYf0s7kjh03rhGqRoz4Nqw5FjnWspM8jPaxx5vhTf6cgH1nVEw8kZAyGg-kIVm5tQNWqRiQ-S-cYslSRjWA5zKzXqqcgwKeSWShLW2aw-XRuSrV9IBOmdGQq2pERdmOAqXTVIKchIwtjPqefKoRqoYe4OZ6h_wlLLnBEFs_BJGv4A9Eabyq07igMiO8NeE8VYMkEhQFl0KlX_VyWmlAm-N28VS8hcg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova
>
>
>
> 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
>
> ___
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>
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[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
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[Freesurfer] question about lesion segmentation using samseg

[Ritobrato Datta]

External Email - Use Caution

Hi All,

I have T1w MPRAGE, T2w and PD images but I dont have FLAIR images from
a Multiple Sclerosis study. Can I use samseg to segment the lesions ?

Can you please suggest ?

Many thanks

Ri
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[Freesurfer] license file error

[Ritobrato Datta]

Hi All,

I am using Mac OS X Sierra and I downloaded free surfer 6 and when running
recon I am getting the following error

reading from IM-0001-0001.dcm...

--

ERROR: Invalid FreeSurfer license key found in license file
/Applications/freesurfer6/.license

  If you are outside the NMR-Martinos Center,

  go to http://surfer.nmr.mgh.harvard.edu/registration.html to

  get a valid license file (it's free).

  If you are inside the NMR-Martinos Center,

  make sure to source the standard environment.

--


The license.txt file is a valid license file and the permissions are set as
follows

-rwxrwxrwx1 root  wheel136 Nov 29 12:48 license.txt


Can you please suggest what seems to be the problem ?


Thanks


Ri
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Mindboggle official software release and publication!

[Ritobrato Datta]

Hi Arno,

This is fascinating stuff. In my research, I have come across instances when I 
felt that a hybrid of ANTS and freesurfer would be very useful. Is this 
pipeline possible for data processed with the earlier versions of freesurfer 
say 5.1 ? FS6 just got released in Jan 2017 and I am sure for most ongoing 
studies, the data have already been processed in earlier versions of 
freesurfer. 

If there is a patch or script to update the data processed using earlier 
versions of freesurfer, that will save a lot of time than running everything 
from scratch in FS6. 

Please let us know. 

Best

Rito
 
- Original Message -
From: Arno Klein 
To: freesurfer@nmr.mgh.harvard.edu
Sent: Thu, 23 Feb 2017 20:37:44 -0500 (EST)
Subject: [Freesurfer] Mindboggle official software release and publication!

Announcing the official release of Mindboggle (http://mindboggle.info),
open source software  and data
 for analyzing the shapes of brain structures from
human MRI data (processed through FreeSurfer and optionally through ANTs).
The release coincides with a publication in PLoS Computational Biology that
documents and evaluates the software:

Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B,
Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human
brains. PLoS Computational Biology 13(3): e1005350.
doi:10.1371/journal.pcbi.1005350


Cheers,
@rno
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Re: [Freesurfer] question about cortical volume group analyses

[Ritobrato Datta]

Dear All,

The email below probably fell through the cracks so I am resending it. 
Appreciate your thoughts and suggestions.

Best

Ri

- Original Message -
From: Ritobrato Datta <rida...@mail.med.upenn.edu>
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Sent: Tue, 17 Jan 2017 14:05:10 -0500 (EST)
Subject: question about cortical volume group analyses

Hi All,

I have a analysed data from AD patients and healthy controls and want to do a 
group analyses of cortical volume. 

I have run qcache on each subject. 

In the lh.volume.fsaverage.mris_preproc.log file,

mri_surf2surf --srcsubject AD1 --srchemi lh --srcsurfreg sphere.reg 
--trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval 
./tmp.mris_preproc.76769/AD1.1.mgh --sval 
/Applications/freesurfer5.1/subjects/AD1/surf/lh.volume --jac --sfmt curv 
--noreshape --no-cortex

what does -jac jacobian correction mean ? Is it accounting/correcting for 
differences in hemispheric volume ?

I want to do a group analyses between AD and controls for cortical volume, can 
I just use the lh.volume.fwhm??.fsaverage.mgh at different smoothing kernels ? 
Do I need to correct for whole brain volume or some scaling or is it already 
taken care of ?

Are there references that have used free surfer to report group analyses for 
cortical volume ? Can someone point to a few ?

Thanks

Ri
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[Freesurfer] question about cortical volume group analyses

[Ritobrato Datta]

Hi All,

I have a analysed data from AD patients and healthy controls and want to do a 
group analyses of cortical volume. 

I have run qcache on each subject. 

In the lh.volume.fsaverage.mris_preproc.log file,

mri_surf2surf --srcsubject AD1 --srchemi lh --srcsurfreg sphere.reg 
--trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval 
./tmp.mris_preproc.76769/AD1.1.mgh --sval 
/Applications/freesurfer5.1/subjects/AD1/surf/lh.volume --jac --sfmt curv 
--noreshape --no-cortex

what does -jac jacobian correction mean ? Is it accounting/correcting for 
differences in hemispheric volume ?

I want to do a group analyses between AD and controls for cortical volume, can 
I just use the lh.volume.fwhm??.fsaverage.mgh at different smoothing kernels ? 
Do I need to correct for whole brain volume or some scaling or is it already 
taken care of ?

Are there references that have used free surfer to report group analyses for 
cortical volume ? Can someone point to a few ?

Thanks

Ri
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Re: [Freesurfer] DTI of frontostriatal tracts

[Ritobrato Datta]

Many thanks. 

Best

Ri

- Original Message -
From: Anthony Dick <ad...@fiu.edu>
To: freesurfer@nmr.mgh.harvard.edu
Sent: Tue, 02 Aug 2016 18:34:53 -0400 (EDT)
Subject: Re: [Freesurfer] DTI of frontostriatal tracts

Hello,

See the paper at this link: http://www.ncbi.nlm.nih.gov/pubmed/25086832

Anthony

> On 8/2/16 12:26 PM, Ritobrato Datta wrote:
>> Hello All,
>>
>> We are studying adolescents with HIV and are interested in 
>> frontostriatal tracts (anything from frontal cortex to 
>> caudate/putamen/nucleus accumbens) and tracts connected to the amygdala.
>>
>> Is anyone aware of DTI based atlases where these tracts are defined 
>> in MNI or some other standard space ?
>>
>> Any suggestions will be very helpful.
>>
>> Best
>>
>> Ri
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>>
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>> whom it is
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>> HelpLine at
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>> you in error
>> but does not contain patient information, please contact the sender 
>> and properly
>> dispose of the e-mail.
>>
>

-- 
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: ad...@fiu.edu
Webpage: http://myweb.fiu.edu/adick
Join the Society for the Study of Human Development: http://www.sshdonline.org

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[Freesurfer] DTI of frontostriatal tracts

[Ritobrato Datta]

Hello All,

We are studying adolescents with HIV and are interested in frontostriatal 
tracts (anything from frontal cortex to caudate/putamen/nucleus accumbens) and 
tracts connected to the amygdala. 

Is anyone aware of DTI based atlases where these tracts are defined in MNI or 
some other standard space ?

Any suggestions will be very helpful.

Best

Ri
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[Freesurfer] white and pail surface editing

[Ritobrato Datta]

Hi All,

We have some subjects who have both wm errors and gm errors. 

Is the following workflow possible


Step 1) control points for the white matter edits. DONT RUN recon-all

Step 2) add the pial surface edits. DONT RUN recon-all

Step 3) Run recon-all to incorporate control points for wm edits (recon-all 
-autorecon2-cp -autorecon3 -subjid cp_before)

AFTER step 3 is COMPLETE, run 

Step 4) Run recon-all to create a fixed pial surface (recon-all -autorecon-pial 
-subjid pial_edits_before)

OR 

Can step 3 and Step 4 be run together as recon-all -autorecon2-cp 
-autorecon-pial -autorecon3 -subjid cp_before

Please let me know.

Thanks

Ri
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[Freesurfer] reference for using T2 to improve pial surface

[Ritobrato Datta]

Hi All,

Can someone point to a reference which shows the advantage of using T2 
alongside T1 to improve the gray - pial boundary ? 

Thank you,

Ri
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[Freesurfer] freesurfer 6 error: dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib

[Ritobrato Datta]

Hello All,

I installed freesurfer 6 on a mac running OS-X Yosemite 10.10.4. I am getting 
the following error when I run recon-all from freesurfer 6. 

Can you please suggest how to fix it ?

Thank you,

Ri

ri@Magi [0] ~/ri/SampleDatasets$ export 
FREESURFER_HOME=/Applications/freesurfer6;export 
SUBJECTS_DIR=/Applications/freesurfer6/subjects;export 
PATH=/Applications/freesurfer6/bin:$PATH;/Applications/freesurfer6/bin/recon-all
 -s Dataset1-only-T1 -i Dataset1/MPRAGE.nii.gz -all
Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20151015
Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20151015
INFO: SUBJECTS_DIR is /Applications/freesurfer6/subjects
Actual FREESURFER_HOME /Applications/freesurfer6
Darwin Magi.uphs.upenn.edu 14.4.0 Darwin Kernel Version 14.4.0: Thu May 28 
11:35:04 PDT 2015; root:xnu-2782.30.5~1/RELEASE_X86_64 x86_64
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_convert
  Reason: image not found
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_convert
  Reason: image not found
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_make_uchar
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_normalize
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_watershed
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_gcut
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_segment
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_label2label
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_em_register
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_ca_normalize
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_ca_register
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_ca_label
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_pretess
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_fill
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_tessellate
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_concatenate_lta
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_normalize_tp2
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_smooth
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_inflate
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_curvature
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_sphere
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_fix_topology
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_topo_fixer
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_ca_label
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_euler_number
  

Re: [Freesurfer] HSF in 5.3

[Ritobrato Datta]

Hello All,

I have run my data through free surfer 5.1. If I run recon-all distributed with 
free surfer 6 as follows

/Applications/freesurfer6/bin/recon-all -s bert -brainstem-structures 

where bert was created using freesurfer 5.1, will it work ?

Best

Ri

- Original Message -
From: Eugenio Iglesias 
To: Alan Francis 
Cc: Freesurfer support list 
Sent: Fri, 11 Dec 2015 12:51:24 -0500 (EST)
Subject: Re: [Freesurfer] HSF in 5.3

Hi Alan, 
the subfield module is not present in 5.3; you'll need to download the 
development version (or wait until 6.0 is released, which should be pretty 
soon=. 
Cheers, 
Eugenio 


Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Alan Francis"  
To: "Freesurfer support list" , "eiglesias" 
 
Sent: Friday, December 11, 2015 6:36:42 PM 
Subject: HSF in 5.3 

Hi Eugenio: 
I am trying to run the HSF method on 42 subjects. The FS version on our cluster 
is 5.3. However when I use the following command I get an error message. 



[alanf@micc alanf]$ recon-all -s Smoke_d004 -hippocampal-subfields 

ERROR: Flag -hippocampal-subfields unrecognized. 

-s Smoke_d004 -hippocampal-subfields 

Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 
x86_64 x86_64 GNU/Linux 




recon-all -s Smoke_d004 exited with ERRORS at Thu Dec 10 16:54:44 EST 2015 




For more details, see the log file 

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 





I tried adding the -hippocampal-subfields-T1 but that did not work too. 




thanks, 




Alan 
-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| 

Alan N . Francis PhD 
NIDA T32 Fellow in Computational Neuroscience 
Brain Imaging Center 
McLean Hospital 
Harvard Medical School 
115 Mill Street, Belmont, MA 02478 
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu 

|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| 
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[Freesurfer] lobar volumes (gm and wm combined)

[Ritobrato Datta]

Hello All,

I am interested in calculating volumes of the frontal / temporal / parietal / 
occipital lobes, gm and wm combined for each lobe. 

Is there a quick way to do that or do I have to add the cortical and the wm 
volumes for all the substructures of each lobe to get the total volume for each 
lobe ?  

Please let me know,

Thanks

Rito
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[Freesurfer] freesurfer pipeline for sub mm voxel resolution

[Ritobrato Datta]

Hi All,

I am working with some 7T data with 0.7 mm isotropic voxels and wanted to know 
if free surfer pipeline (version 5.3) can work these images ? 

I also have FLAIR images and wanted to know if I can use the two to create 
myelin maps ?

Please suggest.

Thanks

Ri
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[Freesurfer] resampling method to transform EPI vol to surf

[Ritobrato Datta]

Hi All,

For a reviewer, I need the following ASAP:

Comments from Reviewer: Please provide a brief description of the resampling 
method by which volume data were transformed to surface data. Was the data 
averaged between the white and pial boundaries? Or was a constant normal 
average taken?

I used bbregister as follows to register the epi image to freesurfer anatomy

bbregister --s $Subject --bold --mov Functional-FS.nii --init-fsl --reg 
FS-register.dat

Can someone comment on the resampling method as the reviewer asked ?

Thanks

Ri
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Re: [Freesurfer] resampling method to transform EPI vol to surf

[Ritobrato Datta]

Hi Thomas,

Thanks for the reply. 

mri_vol2surf --src A042512S.img --srcreg FS-register.dat --hemi rh --projfrac 
0.5 --noreshape --o raA042512S.mgh
srcvol = A042512S.img
srcreg = FS-register.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Reading surface Applications/freesurfer/subjects/A042512S/surf/rh.white
Done reading source surface
Reading thickness Applications/freesurfer/subjects/A042512S/surf/rh.thickness
Done
Mapping Source Volume onto Source Subject Surface
 1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 12943
Writing to raA042512S.mgh
Dim: 136452 1 1

So does this mean the data is getting averaged midway between wm and pial 
boundaries ?

Please let me know, 

Best

Ri


- Original Message -
From: Thomas Yeo ytho...@csail.mit.edu
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Tue, 23 Dec 2014 06:43:40 -0500 (EST)
Subject: Re: [Freesurfer] resampling method to transform EPI vol to surf

Hi Ri,

The command you provide just register (align) the EPI data with the T1
image. It doesn't actually tell us how you sample your data onto the
surface. Presumably you must have used mri_vol2surf (at least
implicitly) to use the resultant registration to sample your data onto
the surface. What is the exact command you use?

Cheers,
Thomas


On Tue, Dec 23, 2014 at 7:26 PM, Ritobrato Datta
rida...@mail.med.upenn.edu wrote:
 Hi All,

 For a reviewer, I need the following ASAP:

 Comments from Reviewer: Please provide a brief description of the resampling 
 method by which volume data were transformed to surface data. Was the data 
 averaged between the white and pial boundaries? Or was a constant normal 
 average taken?

 I used bbregister as follows to register the epi image to freesurfer anatomy

 bbregister --s $Subject --bold --mov Functional-FS.nii --init-fsl --reg 
 FS-register.dat

 Can someone comment on the resampling method as the reviewer asked ?

 Thanks

 Ri
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 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.

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[Freesurfer] dt_recon error

[Ritobrato Datta]

Hi All,

I ran dt_recon and got the following error. Can someone suggest how to fix this 
? I have attached the dwi-infodump.dat file for more information. 

Thanks a lot for the help.

Best

Rito

#@#---
Fitting Tensors
Mon Aug 11 07:29:29 EDT 2014
cd /Users/iron/rito/VisualMeasures-CHOP/VisionMeasures-003
mri_glmfit --y 
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii 
--glmdir /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon --dti 
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat

$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
cwd /Users/iron/rito/VisualMeasures-CHOP/VisionMeasures-003
cmdline mri_glmfit --y 
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii 
--glmdir /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon --dti 
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat
 
sysname  Darwin
hostname magi-2-balthasar.uphs.upenn.edu
machine  x86_64
user iron
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii
logyflag 1
X
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat
usedti  1
glmdir /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory 
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon
Loading y from 
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii
Using DTI
bValue = 1000
ERROR: cannot extract sWiPMemBlock.alFree[8] from 
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat

dwi-infodump.dat
Description: Binary data
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Re: [Freesurfer] Fwd: V1 and V2 labels valid with clinical populations?

[Ritobrato Datta]

Hi Krista,

Please refer to the following publications from Geoff Aguirre's lab -

http://www.ncbi.nlm.nih.gov/pubmed/23041195

http://www.ncbi.nlm.nih.gov/pubmed/24676149

All templates are in fsaverage_sym space in .mgh format and are available for 
download

https://cfn.upenn.edu/aguirre/wiki/public:data_currbio_2012_benson

https://cfn.upenn.edu/aguirre/wiki/public:data_ploscomputbiol_2014_benson

Best

Rito

- Original Message -
From: krista kelly krista.kell...@gmail.com
To: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Mon, 11 Aug 2014 11:45:17 -0400 (EDT)
Subject: [Freesurfer] Fwd: V1 and V2 labels valid with clinical populations?

Just wanted to pose this question again to the Freesurfer community:

Can anyone provide any advice on how to justify using the V1, V2 labels in
FreeSurfer in clinical populations without also collecting functional
retinotopy data?

Thanks!
Krista

-- Forwarded message --
From: krista kelly krista.kell...@gmail.com
Date: Wed, Jun 18, 2014 at 4:51 PM
Subject: Re: [Freesurfer] V1 and V2 labels valid with clinical populations?
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu


OK thanks. I see a lot of pubs using these labels. Can anyone provide any
advice on how to justify using these labels in clinical populations without
also collecting functional retinotopy data?


On Wed, Jun 18, 2014 at 4:13 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:

 Hi Krista

 I don't think we have any idea. The labels are based purely on anatomy, but
 whether those areas keep their functional specification we have no idea.

 let us know if you find out though!
 Bruce
 On Wed, 18 Jun 2014, krista kelly wrote:

  Does anyone know of any support (i.e. articles/data) suggesting that the
 V1
  and V2 labels automatically created in the Freesurfer pipeline,
 especially
  when looking at surface area/gyrification, are valid to use with clinical
  populations? In particular, visually deprived populations?
  Thanks!
  Krista
 
 
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[Freesurfer] primary auditory cortex ROI

[Ritobrato Datta]

Hi All,

My email may have fallen through the cracks over the weekend so I am sending it 
again. 

I need to demarcate primary auditory cortex in a group of subjects anatomically 
and I came across the following papers -

https://surfer.nmr.mgh.harvard.edu/ftp/articles/2013/2013_-_Wasserthal_et_al._-_NeuroImage.pdf

https://surfer.nmr.mgh.harvard.edu/ftp/articles/Sigalovsky_et_al_2006.pdf

Is there a script that I can use on my 3T MPRAGE images to get primary auditory 
cortex ROI ? 

That will be very helpful.

Best,

Ri
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Re: [Freesurfer] primary auditory cortex ROI

[Ritobrato Datta]

Hi Doug,

Wow, telepathy…Just resent my email and got this reply. THanks. I need to 
compute the surface area of primary auditory cortex so was looking for an 
approach similar to the Hinds V1 approach and came across two papers by your 
group. So if I can demarcate A1 based on myelination patterns in T1 MPRAGE 
images from 3T, that will be the best solution. Please let me know if thats 
possible. 

Thanks

Rito


- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Mon, 10 Mar 2014 11:19:07 -0400 (EDT)
Subject: Re: [Freesurfer] primary auditory cortex ROI

We do have a label for transversetemporal. What do you want to do with 
it? You can extract it out of ?h.aparc.annot or aparc+aseg.mgz, 
depending on what you want to do with it
doug


On 03/08/2014 06:48 AM, Ritobrato Datta wrote:
 Hi All,

 I need to demarcate primary auditory cortex in a group of subjects 
 anatomically and I came across the following papers -

 https://surfer.nmr.mgh.harvard.edu/ftp/articles/2013/2013_-_Wasserthal_et_al._-_NeuroImage.pdf

 https://surfer.nmr.mgh.harvard.edu/ftp/articles/Sigalovsky_et_al_2006.pdf

 Is there a script that I can use on my 3T MPRAGE images to get primary 
 auditory cortex ROI ?

 That will be very helpful.

 Best,

 Ri
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-- 
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MGH-NMR Center
gr...@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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[Freesurfer] primary auditory cortex ROI

[Ritobrato Datta]

Hi All,

I need to demarcate primary auditory cortex in a group of subjects anatomically 
and I came across the following papers -

https://surfer.nmr.mgh.harvard.edu/ftp/articles/2013/2013_-_Wasserthal_et_al._-_NeuroImage.pdf

https://surfer.nmr.mgh.harvard.edu/ftp/articles/Sigalovsky_et_al_2006.pdf

Is there a script that I can use on my 3T MPRAGE images to get primary auditory 
cortex ROI ? 

That will be very helpful.

Best,

Ri
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but does not contain patient information, please contact the sender and properly
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[Freesurfer] T1 FLASH parameters for cortical thickness analyses

[Ritobrato Datta]

Hi All,

I have collected T1 3D FLASH on a subject and here are some details of the 
sequence,

Manufacturer = SIEMENS
StudyDescription = Neuro_3T^brain_3t
SeriesDescription = Axial Global FLASH FA27
ManufacturersModelName = Verio
ReferencedImageSequence = 
1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835978\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835980\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835979
ScanningSequence = GR
SequenceVariant = SP
ScanOptions = SAT1
MRAcquisitionType = 3D
SequenceName = *fl3d1
SliceThickness = 1
RepetitionTime = 20
EchoTime = 5
InversionTime = -
NumberofAverages = 1
ImagingFrequency = 123.200338
ImagedNucleus = 1H
EchoNumbers = 1
MagneticFieldStrength = 3
NumberofPhaseEncodingSteps = 192
EchoTrainLength = 1
PercentSampling = 100
PercentPhaseFieldofView = 75
PixelBandwidth = 179
DeviceSerialNumber = 40156
SoftwareVersions = syngo MR B17
ProtocolName = Axial Global FLASH FA27
TransmitCoilName = Body
AcquisitionMatrix = 0\256\192\0
In-planePhaseEncodingDirection = ROW
FlipAngle = 27
VariableFlipAngleFlag = N
SAR = 0.19411263

My questions are the following -

1) Can I get reliable cortical thickness estimates using a T1 3D FLASH sequence 
at 3T Siemens TRIO ?

2) Which version of freesurfer is recommended ?

3) One reason, I collected T1 FLASH is I want to get whole brain volume and 
brain parenchymal fraction in Multiple sclerosis patients. But if freesurfer 
prefers MPRAGES over FLASH for cortical thickness, I am wondering how reliable 
are the standard MPRAGE sequences for calculation of whole brain volume and 
brain parenchymal fractions ?

4) I ran the recon on the FLASH using freesurfer 5.3 and it looks very decent 
but has anyone tested and optimized the parameters for the T1 FLASH sequence 
for cortical thickness estimations ?

5) If you can share your opinion and experiences in this topic and maybe point 
me to some references using flash and freesurfer for cortical thickness, that 
will be very helpful. 

Best

Ri
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Re: [Freesurfer] T1 FLASH parameters for cortical thickness analyses

[Ritobrato Datta]

Hi Bruce,

Thank you for the reply and the suggestions. So if I shorten the TE on the 
FLASH and lengthen the overall scan time, will that help ? I am specifically 
interested in the brain vol (minus CSF) for MS atrophy as well as cortical 
thickness analyses so I am keen to explore the possibility to extract both the 
measures from a single anatomical sequence.  

Please let me know. 

Thanks

Rito

- Original Message -
From: Bruce Fischl fis...@nmr.mgh.harvard.edu
To: Ritobrato Datta rida...@mail.med.upenn.edu
Cc: free surfer freesurfer@nmr.mgh.harvard.edu
Sent: Tue, 10 Dec 2013 13:42:05 -0500 (EST)
Subject: Re: [Freesurfer] T1 FLASH parameters for cortical thickness analyses

Hi Ri

the sequence looks reasonable, although your TE of 5ms is somewhat long 
and will reduce CNR and SNR. Can you shorten it? I would think you should 
be able to. We looked at this for a while, and in the end the mprage 
outperformed FLASH in terms of cortical gray matter/cerebral white matter 
CNR/unit time. The FLASH scans were ok, but not as good as mprage. I think 
either is fine for ICV, although if you collect a lower fiip FLASH which 
will be PD weighted (e.g. a 5deg) then that will be an advantage for ICV.

cheers
Bruce


On Tue, 10 Dec 2013, 
Ritobrato Datta wrote:

 Hi All,

 I have collected T1 3D FLASH on a subject and here are some details of the 
 sequence,

 Manufacturer = SIEMENS
 StudyDescription = Neuro_3T^brain_3t
 SeriesDescription = Axial Global FLASH FA27
 ManufacturersModelName = Verio
 ReferencedImageSequence = 
 1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835978\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835980\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.301311221946159835979
 ScanningSequence = GR
 SequenceVariant = SP
 ScanOptions = SAT1
 MRAcquisitionType = 3D
 SequenceName = *fl3d1
 SliceThickness = 1
 RepetitionTime = 20
 EchoTime = 5
 InversionTime = -
 NumberofAverages = 1
 ImagingFrequency = 123.200338
 ImagedNucleus = 1H
 EchoNumbers = 1
 MagneticFieldStrength = 3
 NumberofPhaseEncodingSteps = 192
 EchoTrainLength = 1
 PercentSampling = 100
 PercentPhaseFieldofView = 75
 PixelBandwidth = 179
 DeviceSerialNumber = 40156
 SoftwareVersions = syngo MR B17
 ProtocolName = Axial Global FLASH FA27
 TransmitCoilName = Body
 AcquisitionMatrix = 0\256\192\0
 In-planePhaseEncodingDirection = ROW
 FlipAngle = 27
 VariableFlipAngleFlag = N
 SAR = 0.19411263

 My questions are the following -

 1) Can I get reliable cortical thickness estimates using a T1 3D FLASH 
 sequence at 3T Siemens TRIO ?

 2) Which version of freesurfer is recommended ?

 3) One reason, I collected T1 FLASH is I want to get whole brain volume and 
 brain parenchymal fraction in Multiple sclerosis patients. But if freesurfer 
 prefers MPRAGES over FLASH for cortical thickness, I am wondering how 
 reliable are the standard MPRAGE sequences for calculation of whole brain 
 volume and brain parenchymal fractions ?

 4) I ran the recon on the FLASH using freesurfer 5.3 and it looks very decent 
 but has anyone tested and optimized the parameters for the T1 FLASH sequence 
 for cortical thickness estimations ?

 5) If you can share your opinion and experiences in this topic and maybe 
 point me to some references using flash and freesurfer for cortical 
 thickness, that will be very helpful.

 Best

 Ri
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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
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Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

[Ritobrato Datta]

ic thats rightI was getting confused. So the total gm vol includes 
cerebellar gm vol but the cortical wm vol only includes the wm vol under the 
cortical ribbon and around the subcortical gm structures?  Or does that 
include wm under the cerebellar cortex as well ?

Is there a table somewhere which specifies which of these freesurfer 
parcellated structures contribute to these combined measures such has 
supratentorial vol / whole gm vol etc etc

That will be very helpful. 



- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Ritobrato Datta rida...@mail.med.upenn.edu, Freesurfer@nmr.mgh.harvard.edu
Sent: Mon, 03 Jun 2013 12:59:30 -0400 (EDT)
Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
brain vol.


Hi Rito, I don't think we report a total wm volume, do we?
doug




On 06/03/2013 12:56 PM, Ritobrato Datta wrote:
 Hi Doug,

 Just following up on your reply sometime back -
 Does total white volume include cerebellar wm vol also ?

 Please let me know.

 Thanks

 Rito

 - Original Message -
 From: Douglas N Greve gr...@nmr.mgh.harvard.edu
 To: freesurfer@nmr.mgh.harvard.edu
 Sent: Fri, 24 May 2013 17:36:18 -0400 (EDT)
 Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
 brain vol.

 Total Gray includes the cerebellar gray
 doug
 On 05/24/2013 03:51 PM, Ritobrato Datta wrote:
 Hello All,

 Can someone address the following ? I sent this query yesterday but it fell 
 through the cracks.

 I am using freesurfer 5.1 for my analysis.

 I am interested in calculating the whole brain vol (total Gray vol + total 
 WM vol) excluding the CSF volume and cerebellum.

 Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol

 In all of the 79 subjects, when I compare the Total Brain Vol to 
 SupraTentorialVol, I find SupraTentorialVol is smaller than the Total Brain 
 Vol I have calculated.

 Here are some measures -

 For 79 subjects -

 Average Total Brain Vol = 1038395.291

 Average SupraTentorialVol = 979996.4684

 Is that expected ?

 Is it possible that CSF vol is part of Total Brain Vol ?

 Any insight will be helpful.

 Thanks

 Rito

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 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
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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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Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

[Ritobrato Datta]

Hi Doug,

I looked that the morphometryStats table that you sent and looks like I need 
the following measure.

BrainSegNotVent - this I believe doesnt include cerebellum etc and no 
ventricles.

But all my data are run through 5.1. How do I get this measure ? If I run the 
5.2 version of mri_segstats on the data that has been run through 5.1, will it 
generate this volume ?

Please let me know and sorry to keep pestering this. 

Thanks

Rito


- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Ritobrato Datta rida...@mail.med.upenn.edu
Cc: Freesurfer@nmr.mgh.harvard.edu
Sent: Mon, 03 Jun 2013 13:54:01 -0400 (EDT)
Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
brain vol.

no, it does not include cerebellum
On 06/03/2013 01:42 PM, Ritobrato Datta wrote:
 In the website below,
 lhCorticalWhiteMatter,rhCorticalWhiteMatter,CorticalWhiteMatter - volume 
 inside the white surface minus anything that is not WM. CorticalWhiteMatter 
 includes hypointensities. This uses the surface-based volume computation for 
 part of the calculation and counts voxels to subtract anything not in WM. 
 It is approximately equal to the count of WM voxels in aparc+aseg.mgz.

 Since, cerebellar wm is in the aparc+aseg.mgz so that means its included in 
 the CorticalWhiteMatter, correct ?

 - Original Message -
 From: Douglas N Greve gr...@nmr.mgh.harvard.edu
 To: Ritobrato Datta rida...@mail.med.upenn.edu
 Cc: Freesurfer@nmr.mgh.harvard.edu
 Sent: Mon, 03 Jun 2013 13:19:54 -0400 (EDT)
 Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
 brain vol.


 See if this answers your question
 http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
 this is for v5.2 and beyond

 On 06/03/2013 01:07 PM, Ritobrato Datta wrote:
 ic thats rightI was getting confused. So the total gm vol includes 
 cerebellar gm vol but the cortical wm vol only includes the wm vol under the 
 cortical ribbon and around the subcortical gm structures?  Or does that 
 include wm under the cerebellar cortex as well ?

 Is there a table somewhere which specifies which of these freesurfer 
 parcellated structures contribute to these combined measures such has 
 supratentorial vol / whole gm vol etc etc

 That will be very helpful.



 - Original Message -
 From: Douglas N Greve gr...@nmr.mgh.harvard.edu
 To: Ritobrato Datta rida...@mail.med.upenn.edu, 
 Freesurfer@nmr.mgh.harvard.edu
 Sent: Mon, 03 Jun 2013 12:59:30 -0400 (EDT)
 Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
 brain vol.


 Hi Rito, I don't think we report a total wm volume, do we?
 doug




 On 06/03/2013 12:56 PM, Ritobrato Datta wrote:
 Hi Doug,

 Just following up on your reply sometime back -
 Does total white volume include cerebellar wm vol also ?

 Please let me know.

 Thanks

 Rito

 - Original Message -
 From: Douglas N Greve gr...@nmr.mgh.harvard.edu
 To: freesurfer@nmr.mgh.harvard.edu
 Sent: Fri, 24 May 2013 17:36:18 -0400 (EDT)
 Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
 brain vol.

 Total Gray includes the cerebellar gray
 doug
 On 05/24/2013 03:51 PM, Ritobrato Datta wrote:
 Hello All,

 Can someone address the following ? I sent this query yesterday but it 
 fell through the cracks.

 I am using freesurfer 5.1 for my analysis.

 I am interested in calculating the whole brain vol (total Gray vol + total 
 WM vol) excluding the CSF volume and cerebellum.

 Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol

 In all of the 79 subjects, when I compare the Total Brain Vol to 
 SupraTentorialVol, I find SupraTentorialVol is smaller than the Total 
 Brain Vol I have calculated.

 Here are some measures -

 For 79 subjects -

 Average Total Brain Vol = 1038395.291

 Average SupraTentorialVol = 979996.4684

 Is that expected ?

 Is it possible that CSF vol is part of Total Brain Vol ?

 Any insight will be helpful.

 Thanks

 Rito

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 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 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.


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[Freesurfer] Repost: question abt supratentorial vol and total brain vol.

[Ritobrato Datta]

Hello All,

Can someone address the following ? I sent this query yesterday but it fell 
through the cracks. 

I am using freesurfer 5.1 for my analysis.

I am interested in calculating the whole brain vol (total Gray vol + total WM 
vol) excluding the CSF volume and cerebellum. 

Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol 

In all of the 79 subjects, when I compare the Total Brain Vol to 
SupraTentorialVol, I find SupraTentorialVol is smaller than the Total Brain Vol 
I have calculated. 

Here are some measures -

For 79 subjects - 

Average Total Brain Vol = 1038395.291

Average SupraTentorialVol = 979996.4684

Is that expected ?

Is it possible that CSF vol is part of Total Brain Vol ?

Any insight will be helpful.

Thanks

Rito

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[Freesurfer] question abt supratentorial vol and total brain vol.

[Ritobrato Datta]

Hello All,

I am using freesurfer 5.1 for my analysis.

I am interested in calculating the whole brain vol (total Gray vol + total WM 
vol) excluding the CSF volume and cerebellum. 

Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol 

In all of the 79 subjects, when I compare the Total Brain Vol to 
SupraTentorialVol, I find SupraTentorialVol is smaller than the Total Brain Vol 
I have calculated. 

Here are some measures -

For 79 subjects - 

Average Total Brain Vol = 1038395.291

Average SupraTentorialVol = 979996.4684

Is that expected ?

Is it possible that CSF vol is part of Total Brain Vol ?

Any insight will be helpful.

Thanks

Rito

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[Freesurfer] question abt optic chaism volume

[Ritobrato Datta]

Hi All,

I am using freesurfer 5.1 for my analysis. In FS 5.1, does the Supratentorial 
volume include the Optic chaism volume ? 

Please let me know. 

Thanks

Ri
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[Freesurfer] brain parenchymal fraction calculation

[Ritobrato Datta]

Hi All,

I am using freesurfer 5.1 and I want to compute the brain parenchymal fraction 
(GM+WM/GM+WM+ventricularCSF). 

In aseg.stats, I get the whole GM vol and I can also get the total ventricular 
CSF by adding the vols of different ventricles. 

But I am confused abt the terminology - CorticalWhiteMatterVol

is this volume the total white matter in the brain or does this exclude 
something ? 

Please advise. 

Best

Ri
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[Freesurfer] question abt dt-recon

[Ritobrato Datta]

Hello All,

I havent used dt-recon yet but I have a question abt it. 

When the dt-recon computes the FA maps, whats the dimensions of these FA maps ? 
Are they resampled to the freesurfer anatomical voxel size (1x1x1) or are they 
in their native voxel size (in which they were collected) ?
If I want to extract say the meanFA from one of the ROIs that freesurfer dumps 
in aseg/wmparc, can I do that ?

Thanks

Ri
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Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

[Ritobrato Datta]

I concur. I have seen similar results in primary visual cortex from ~40 
subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to 1.9 in 
V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3.

Ritobrato Datta, Ph.D.
Post Doctoral Researcher
Department of Neurology
University of Pennsylvania School of Medicine
3rd Floor, Room 312
3710 Hamilton Walk (Goddard Laboratories)
Philadelphia, PA 19104-6241
email - rida...@mail.med.upenn.edu
 

- Original Message -
From: Daniel Yang yung-jui.y...@yale.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT)
Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0

Dear FreeSurfer Experts,

I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161 subjects, 
and I'm interested in rh_superior_temporal_sulcus_thickness in particular.

Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in 5.2.0. 
They are significantly different, t(160) = 56.71.

The correlation between the two versions is r = .33

Is this something possible?? I can't see what went wrong in my procedures.

Thanks!
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

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[Freesurfer] optic radiation ROI

[Ritobrato Datta]

Hi All,

Is there an Optic Radiation ROI in freesurfer or some other program ? 
Please let me know.

Thank you

Ri
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[Freesurfer] tkregister2 error on lion

[Ritobrato Datta]

Hi All,

I have freesurfer 5.1 installed on my laptop running Lion. When I tried to use 
tkregister2, the program doesnt load up the GUI. It failed even after 
installing XQuartz. 
It loaded successfully in a machine running Snow Leopard. 
Any suggestions on how to get around it or are there any fixes available ?

Thanks a lot

Ri
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[Freesurfer] color table for custom labels

[Ritobrato Datta]

Hello All,

I have created some labels and want to assign distinct colors to each and save 
it so that I can assign the same colors when I load them again. How do I do it 
? 

Thanks

Ri
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[Freesurfer] masking ?h.curv with a label

[Ritobrato Datta]

Hi,

I have created a ?.cortex.label on canine brain. How do I apply this label to 
the ?h.curv and ?.sulc so that I get rid of the medial wall FOREVER ?

Thanks a lot

Ri
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[Freesurfer] length of a label

[Ritobrato Datta]

Hi All, 

Is there a way to calculate the length and width of a label ?
Please let me know. 
Thanks a lot

Ri

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[Freesurfer] setting a cluster size and thresholding in tksurfer

[Ritobrato Datta]

Hi

I am displaying the fMRI results in tksurfer. Is there a way in tksurfer to set 
a cluster size (for eg 50 vertices) and display only those activated regions 
which have bigger clusters than 50 ?

Thanks

Ri
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[Freesurfer] error while dividing an annotation/label

[Ritobrato Datta]

Hello,

I am trying to divide lh.v1.predict.label into equal parts. So I did the 
following -


A) Created a colorfile V1color.ctab which contains the following-

#
#No. Label Name:R   G   B   A
1   V170  130 180 1



B) mris_label2annot --s 001raw --h lh --ctab V1color.ctab --a TrialV1 --l 
lh.v1.predict.label --maxstatwinner

C) echo V1 4   splittable.txt


D) mris_divide_parcellation 001raw lh TrialV1.annot splittable.txt 
lh.TrialV1.split

reading colortable from annotation file...
colortable with 2 entries read (originally V1color.ctab)
interpreting 4th command line arg as split file name
dividing V1 (1) into 4 parts
allocating new colortable with 4 additional units...
Segmentation fault

What am I doing wrong and how do I correct it ?

Thanks

Ri
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[Freesurfer] dividing a label into equal parts

[Ritobrato Datta]

Is there a way to divide a surface label like V1 into equal parts (say 10 
parts) either along its length or width and save each part as a separate label 
? Drawing them in tkmedit is quite crude and not very accurate. 

Please let me know.

Thanks

Ri
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[Freesurfer] normalised functional volumetric data to fsaverage

[Ritobrato Datta]

Hi All,

I have some functional beta maps normalised to the T1 template using spm8 and I 
am wondering how to map them onto the fsaverage surface ? 

In native subject space, I pipe a functional scout image into bbregister to get 
a registration matrix which is then used to map volumetric beta maps to native 
freesurfer surface and fsaverage surface.

How do I do this with the normalised functional data ?

Thanks

Ri

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[Freesurfer] defining our own regions for tractography

[Ritobrato Datta]

Hello All,

I am a total newbee in dt-recon and tracula. So sorry if this is a very basic 
question. 

From what I gathered so far-

TRACULA uses the aparc+aseg.mgz from the FreeSurfer recon (T1-weighted volume) 
as ROIs to construct the tracts and also constructs a few tracts by default.

Is there a way of defining our own ROIs and get tracts ?

Thanks

Ri


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[Freesurfer] distortion metric question

[Ritobrato Datta]

Hi All,

Is there a way to examine the distortion metric of the freesurfer surface 
normalization ? 
Please let me know.
Thanks

Ri
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Re: [Freesurfer] what is thalamus-proper and clusters-table related question

[Ritobrato Datta]

Actually I have the same question - does the thalamus proper include LGN ?

- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Tetiana Dadakova tetian...@gmail.com
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, September 2, 2011 12:28:45 PM
Subject: Re: [Freesurfer] what is thalamus-proper and clusters-table related 
question

I'm not sure about #1, maybe BF can chime in.

Tetiana Dadakova wrote:
 Dear FS list,

 1. What does a label Thalamus Proper include? Is it the same as thalamus?

 2. After correcting for multiple comparisons, I get a table of
 clusters. I have several questions regarding this table: What do the
 columns Max, CWPLow, and CWPHigh represent? 
  1. CWP - cluster-wise pvalue. The pvalue of the cluster corrected for
 multiple comparisons
  2. CWPLow - lower 90% confidence limit of CWP based on binomial 
distribution
  3. CWPHi  - upper 90% confidence limit of CWP based on binomial 
distribution

 Regarding the NVtxs
 column: is it the number of vertexes in cluster?  
Yes
 What kind of information can I get from this value? 
It is not very informative so don't feel like you have to use it. It is 
good for assuring that the software is doing the right thing.
 If two clusters have different areas but the same number of vertexes, does it 
 mean something?
   
It means that the area of the component triangles that make up the 
vertices is different.

doug
 Thank you very much for your help and for your time,
 Tanja.
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[Freesurfer] thalamic segmentations in freesurfer

[Ritobrato Datta]

Hello All,

I noticed the following in FreeSurferColorLUT.txt

8001  Thalamus-Anterior 74  130 181 0
8002  Thalamus-Ventral-anterior 242 241 240 0
8003  Thalamus-Lateral-dorsal   206 65  78  0
8004  Thalamus-Lateral-posterior120 21  133 0
8005  Thalamus-Ventral-lateral  195 61  246 0
8006  Thalamus-Ventral-posterior-medial 3   147 6   0
8007  Thalamus-Ventral-posterior-lateral220 251 163 0
8008  Thalamus-intralaminar 232 146 33  0
8009  Thalamus-centromedian 4   114 14  0
8010  Thalamus-mediodorsal  121 184 220 0
8011  Thalamus-medial   235 11  175 0
8012  Thalamus-pulvinar 12  46  250 0
8013  Thalamus-lateral-geniculate   203 182 143 0
8014  Thalamus-medial-geniculate42  204 167 0

Are these generated by the cross-sectional recon-all or are these futuristic ?

If they are available how do I view them ?

Please let me know.

Thanks

Ri
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[Freesurfer] Periaqueductal gray ROI

[Ritobrato Datta]

Hi All,

Is there a Periaqueductal Gray ROI generated by freesurfer recon ? 

Please let me know. 

Thanks

Ri

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[Freesurfer] V1 on fsaverage

[Ritobrato Datta]

Hi 

Is it possible to estimate the V1 boundary on fsaverage using Hinds method ?

Thanks

Ri
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[Freesurfer] outline of a label as an overlay

[Ritobrato Datta]

Hello All,

Is there a way to save the outline of a label as an overlay (say .mgh file) ?

Please let me know.

Thanks

Ri
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[Freesurfer] V1 dimensions

[Ritobrato Datta]

Hello All,

Is there a way to calculate the length and breadth of V1 in mm defined by the 
Fischl method ? How do I do it ?

Thanks

Ri
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[Freesurfer] gyrification Index of a label

[Ritobrato Datta]

Hi All,

I have run

recon-all -s subj -localGI

Now I want to get the gyrification Index of a particular label. Is there a way 
to do that ?

Please let me know 

Thanks

Ri

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[Freesurfer] stats on masked functional data

[Ritobrato Datta]

Hello All,

Looks like this question slipped through. 
I have a functional beta value overlay as a .mgh file and a V1 label file and I 
want to compute the average beta value within that mask for each subject. 

How do I do this ?

Thanks a lot

Ri
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[Freesurfer] stats on masked functional data

[Ritobrato Datta]

Hello All,

I have a functional beta value overlay as a .mgh file and a label file and I 
want to compute the average value within that mask for each subject. 

Is there a program to do that ?

Thanks

Ri
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[Freesurfer] question abt fsaverage V1

[Ritobrato Datta]

Hello All,

I noticed that that there is a fsaverage/label/?h.V1.label

Is this label created from the Hinds and Fischl method ? Can someone give some 
details abt it ?

Also for individual subjects, when I run the V1 estimation using Hinds and 
Fischl method, how accurate are the V1 / V2 border compared to retinotopy ? Or 
which is more accurate ?

Thanks

Ri
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Re: [Freesurfer] flattenning question

[Ritobrato Datta]

Continuing the conversation, if I have a flattened patch like an occipital 
patch, and i manually draw a label on it and save it, can I then use 
mri_label2label to map it to other subjects ?

Thx

Ri

- Original Message -
From: Bruce Fischl fis...@nmr.mgh.harvard.edu
To: Gabriel Go.Es. gabriel...@hotmail.com
Cc: free surfer freesurfer@nmr.mgh.harvard.edu
Sent: Friday, May 20, 2011 8:26:40 AM
Subject: Re: [Freesurfer] flattenning question

Hi Gabriel

you cut the patch out in tksurfer first, then call mris_flatten. For 
small patches such as occipital ones we typically use the -complete 
option these days which minimizes the complete distance distortion matrix.

cheers
Bruce


On Fri, 20 May 2011, Gabriel Go.Es. wrote:


 Dear FreeSurfers

 I'm wondering about the flattenning options of FS I've saw that the 
 mris-flatten command does the trick but, it asks for a patch, my questions 
 are: can I flat any cortical region? and, how do I create a patch to 
 mris_flatten?

 Thanks in advanced,
 Gabriel



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[Freesurfer] different V1 sizes for same subject in two different sessions

[Ritobrato Datta]

Hello All,

I have estimated V1 using Hinds and Fischl method for some subjects scanned on 
two different days. I've been going through the V1 surface area data for these. 
One thing that concerns me is that is seems that very different V1 sizes are 
reported for the same subject when scanned on different dates and each run 
through the cross sectional stream.
I am trying to check the test-re-test values for these.

Any idea why this is so and whats a better method to do the comparison ?

Thanks

Ri


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[Freesurfer] .mgh to .label ??

[Ritobrato Datta]

Hello All,

How do I convert an .mgh file (my .mgh file is a binary mask) onto a label ? Is 
there an automated way other than drawing ?

Thanks

Ri
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[Freesurfer] effect size for cortical thickness changes

[Ritobrato Datta]

Hello All,

Are there reports of studies of cortical thickness changes using freesurfer 
which report effect sizes for the ROIs of interest ie how much of a change in 
millimeters was observed as opposed to p-values reported.

Please let me know.

Thanks a lot

Ri
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[Freesurfer] way to binarize MGH file

[Ritobrato Datta]

Hi All,

I am looking for a way to binarize MGH files.

I took a mask I made in volumetric space to surface space, and I want to 
binarize it so it doesnt contain decimal values. What is the command?

Will mri_binarize work on mgh files ? I need to manipulate MGH files, with the 
same output type.

Please let me know.

Thx

Ri
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[Freesurfer] laterality analysis

[Ritobrato Datta]

Hello All,

I am trying to do a laterality analysis for a cortical reorganization project 
in blind patients. Since each hemisphere has slightly different gyral and 
sulcal patterns, in theory, one hemisphere could be mirrored and compared; in 
the surface space this amounts to turning one of the spheres inside-out (so to 
speak). 

Are there are any extant tools available to do this for freesurfer ? 

I remember seeing something in the discussion boards in the past. 
Please let me know. 

Thank you very much

Ri
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[Freesurfer] freesurfer and VBM

[Ritobrato Datta]

Hello All,

Are there any papers comparing freesurfer to VBM ?

Can anyone point me to them ?

Thanks

Ri
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[Freesurfer] black background to white in tksurfer

[Ritobrato Datta]

Is there a way to set the black background to white in tksurfer ?

Thanks

Ri

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[Freesurfer] occipital label without v1

[Ritobrato Datta]

Hello All,

I have an occipital label and a v1 label and I have created binary masks from 
them. Is there a way to create an Occipital label - V1 label ie excluding v1 
from occipital label.

Please let me know.

Thank you

Ri
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[Freesurfer] mask.mgh to volume

[Ritobrato Datta]

Hello All ,

I have a binary mask - mask.mgh. 

I want create a binary volumetric mask from it in the same space and dimension 
as orig.mgz

Can mri_label2vol be used ? How ? If not, how can this be done ?

Thanks a lot

Ri
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[Freesurfer] --sfmt curv flag

[Ritobrato Datta]

Hello All,

I posted this question yesterday. It probably got lost. So I am posting again. 

For functional data to be resampled to fsaverage using mri_surf2surf what 
should be used with  --sfmt  flag ?

For the thickness the --sfmt curv is used when running qcache.

Thanks

Ri

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[Freesurfer] converting label to binary mask.mgh

[Ritobrato Datta]

Hello All,

I have created a V1 label using Hinds and Fischl Method. Is a label a .mgh file 
as well ?? 

How do I convert this label to a binary mask mgh file ?

Please let me know.

Thanks much

Rito

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[Freesurfer] volumetric version of fsaverage brain

[Ritobrato Datta]

Hello All,

Which is the volumetric version of the fsaverage brain in freesurfer ? Can you 
tell me what is it called ? 

Thanks

Ri



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[Freesurfer] LGN label or ROI....

[Ritobrato Datta]

Hi All, 

Is there a method for obtaining an ROI for the lateral geniculate nucleus in 
freesurfer ?

Thanks,

Ri

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[Freesurfer] question abt mri_vol2surf....

[Ritobrato Datta]

Hello All,

I have a simple question. I have functional data (3 mm cubic voxels) from 20 
subjects that I am using mri_vol2surf to resample on the fsaverage surface. I 
want to run qdec or mri_glmfit on these data. In order to do grp stats with 
functional data, what surface do I need to specify in the '--surf' flag ? Does 
it matter ?

Thanks

Ri
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Re: [Freesurfer] question abt mri_vol2surf....

[Ritobrato Datta]

ok thats what i thought but just wanted to double check...
Thx


- Original Message -
From: Nick Schmansky ni...@nmr.mgh.harvard.edu
To: Ritobrato Datta rida...@mail.med.upenn.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, February 16, 2010 12:58:07 PM GMT -05:00 US/Canada Eastern
Subject: Re: [Freesurfer] question abt mri_vol2surf

the default surf is the 'white' surf, but this only means the
coordinates in the output surface file will have the white surface
coordinates.  the vertices still remain one-to-one matched between the
white-pial-and-inflated-(and-sphere), so the -surf arg is irrelevant for
your group analysis.

n.

On Tue, 2010-02-16 at 10:04 -0500, Ritobrato Datta wrote:
 Hello All,
 
 I have a simple question. I have functional data (3 mm cubic voxels) from 20 
 subjects that I am using mri_vol2surf to resample on the fsaverage surface. I 
 want to run qdec or mri_glmfit on these data. In order to do grp stats with 
 functional data, what surface do I need to specify in the '--surf' flag ? 
 Does it matter ?
 
 Thanks
 
 Ri
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[Freesurfer] commandline tools to create .mgh files from .nii files.....

[Ritobrato Datta]

Hello All,

Are there commandline tools to take processed functional data in .nii format 
and overlay it on the inflated or spherical surface and output a .mgh file ?
I want to specify the registration method as Calculate identity matrix

Thanks

Rito
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[Freesurfer] thickness map from a label

[Ritobrato Datta]

Hello All,

I have created some surface labels and want to create corresponding thickness 
maps (Not stats). Is there a way to do that ? 

Thanks

Ri

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[Freesurfer] aparcstats2table for std dev associated with av thickness

[Ritobrato Datta]

Hi all

Is there a way to create a multi subject table of the std dev associated with 
av thickness using aparcstats2table or for that matter any way to create a 
table similar to the outout of aparcstats2table ?

Thanks

Ri
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[Freesurfer] combining multiple labels to a single label

[Ritobrato Datta]

Hi all,

Is there a way / program to specify and combine multiple labels to create a 
single label ? 

Please let me know.

Thanks a lot

Ri
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[Freesurfer] annot to label to gm thickness map

[Ritobrato Datta]

Hello All, 

I want to create a gm thickness map from central sulcus and precentral gyrus. I 
plotted the lh.aparc.a2005s.annot on the inflated surface and I see the sulci 
and gyri. 

Is there a way to create a binary label of the central sulcus and precentral 
gyrus ? Can that label be then used to create a thickness map ?

Please let me know ?

Thanks

Rito

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[Freesurfer] talairach failure

[Ritobrato Datta]

Hello All,

I ran recon-all on a subject and got the following error

talairach_avi done

cp transforms/talairach.auto.xfm transforms/talairach.xfm 

#
#...@# Talairach Failure Detection Thu Nov 19 16:17:54 EST 2009
/jet/subjects/MC/mri

talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
***FAILED*** (p=0., pval=0.  threshold=0.0050)

recon-all exited with ERRORS at Thu Nov 19 16:17:55 EST 2009
===END LOG FILE===

The brain is quite rotated from upright alignment, which is likely the problem. 
Any suggestions on how to do it or whether I should ?

Thanks 

Ri
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[Freesurfer] structural morphometric analyses for 50 subjects

[Ritobrato Datta]

Hello All,

I have processed about 100 datasets with recon-all (autorecon1, 2and 3)

There are 50 subjects, each subject is scanned twice, 19 months apart. So each 
subject acts as their own control. We only have structural data for these 
subjects only MPRAGES, one per each scan. No functional data. 

What kind of structural morphometric analyses can I do using freesurfer ? I 
mean if I want to see what has changed in each subject between the two sessions 
?
 
For each session, we have other data like their blood pressure, gender, age, 
ambient pressure, ambient temperature etc. For eg, there is a difference in 
ambient temperature between the first and second scans and I want to see if 
there is a structural morphometric change in each subject due to this 
temperature change, can that kind of statistics be done with freesurfer ? How 
do I remove the effect of other factors to see only the changes due to 
temperature change ? 

I have never done this kind of an analyses before, so so maybe freesurfer 
already has a pipe for this sort of analyses. I dont know. I am looking for any 
guidance I can get. 

Please let me know.

Thanks a lot,
 
Rito
 
 
 
Ritobrato Datta, Ph.D.
Post Doctoral Fellow
Department of Neurology
Center for Functional Neuroimaging
University of Pennsylvania School of Medicine
3rd Floor Gates Building
3400 Spruce St. 
Philadelphia
Pa 19104




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[Freesurfer] question abt mri_surf2surf usage

[Ritobrato Datta]

Hello All,

I am confused abt the sage of mr_surf2surf.

I have 3 subjects. All three have been piped through freesurfer autorecon-all.

So i have subj? ?h sphere.reg

I also have functional data for the 3 subjects overlaid on the subj? ?h 
sphere.reg and I saved them as .mgh files.

I want to map subj2.mgh and subj3.mgh to subj1 ?h sphere.reg

How do I do that ? 

I looked at the mri_surf2surf usage but got confused.

Please let me know.

Thanks a lot

Ri
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[Freesurfer] transforming of the spherical atlas Right -- Left hemisphere ??

[Ritobrato Datta]

Hello All,

we are considering combining some data from the left and right hemispheres. Is 
there a way to implement a transform of the spherical atlas Right -- Left 
hemisphere? Topologically, this probably corresponds to turning the sphere 
inside-out (plus registration of residual hemispheric differences in gyral 
pattern).

Please let me know if there are ways to do this.

Thanks

Ri
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Re: [Freesurfer] problem with intensity normalization control points

[Ritobrato Datta]

Thx Nick for the reply. 

Then how do I make sure that the spline (that I have used control points to 
demarcate) is included in the white matter boundary ?

Ri

- Original Message -
From: Nick Schmansky ni...@nmr.mgh.harvard.edu
To: Bruce Fischl fis...@nmr.mgh.harvard.edu
Cc: Ritobrato Datta rida...@mail.med.upenn.edu, freesurfer 
freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, September 8, 2009 1:45:04 PM GMT -05:00 US/Canada Eastern
Subject: Re: [Freesurfer] problem with intensity normalization control points

Ritobrato,

The control points mark voxels as belonging to white matter, and should
be marked sparingly.  They are not points on a spline, as it appears you
were trying to do in the image.

Nick

On Tue, 2009-09-08 at 13:39 -0400, Bruce Fischl wrote:
 Hi Ri,
 
 you have to be careful to only put the control points in voxels that are 
 completely white matter (no partial voluming). I also don't know what you 
 mean by the control points didnt get converted to a continuous line. Can 
 you elaborate?
 
 cheers,
 Bruce
 On 
 Tue, 8 Sep 2009, Ritobrato Datta wrote:
 
  Hello All,
 
  I followed the steps in exercise C in the following page 
  http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints
  and added control points manually and then saved the Control Points by File 
   Save Control Points
 
  Then I ran recon-all -autorecon2-cp -autorecon3 -s subjid
 
  After completion, I opened the viewer to check if it is implemented by 
  tkmedit subjid brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white
 
  But saw that the image where I added the control points didnt get converted 
  to a continuous line. I have attached a figure as an illustration. What am 
  I doing wrong ?
 
  Thanks
 
  Ri
 
 
 
 
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[Freesurfer] converting .img to .nii

[Ritobrato Datta]

Hello All, 

I am trying to convert 

[...@home] /jet/subjects/002/Anatomy mri_convert nAnatomical_fsl_FLOAT.img 
nAnatomical_fsl_FLOAT.nii
mri_convert nAnatomical_fsl_FLOAT.img nAnatomical_fsl_FLOAT.nii 
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from nAnatomical_fsl_FLOAT.img...
-
INFO: could not find /jet/subjects/002/Anatomy/nAnatomical_fsl_FLOAT.mat file 
for direction cosine info.
INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in 
/jet/subjects/002/Anatomy/nAnatomical_fsl_FLOAT.mat file
-
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to nAnatomical_fsl_FLOAT.nii...

It wrote the .nii file and it looks the same as the .img qualitatively, but I 
just thought I ask if I need the .mat file or if there is a better way to 
compare whether the conversion worked correctly. 
Please let me know.

Thx

Ri

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[Freesurfer] running freesurfer after talairach touch-ups...

[Ritobrato Datta]

Hello all,

I ran 

recon-all -autorecon-all -s subjid

After it ran all the way through, I ran 

tkregister2 --mgz --s subjid --fstal --surf orig

and saved everything with the SAVE REG button in the tkregister2 toolbar.

Since I initially ran all the steps before the talairach touch-ups, what do I 
run to re-process the data and re-write with the new talairach modifications ? 
Do I have to use ' -force ' with the command ?

I have a same question for the step, Using Control Points to Fix Intensity 
Normalization. What command do I run after I am done adding control points ? 

Thanks

Ri
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[Freesurfer] read in .vtk files ?

[Ritobrato Datta]

Hello All,

Can freesurfer read in .vtk surface files ? 

Please let me know.

Thanks

Ri

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[Freesurfer] question abt inflated brain registration

[Ritobrato Datta]

Hello All, 

I am new to freesurfer. Is there a method to create a registered inflated 
brain from the lh.sphere.reg (which if I understood correctly, is the 
?h.sphere data for a subject registered to the spherical atlas). If yes, is it 
also possible to display the corresponding functional data on this registered 
inflated brain ? 
Please let me know. 

Thanks

Ri

Ritobrato Datta, Ph.D.
Post Doctoral Fellow
Department of Neurology
University of Pennsylvania School of Medicine
3rd Floor Gates Building
3400 Spruce St. 
Philadelphia
Pa 19104


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[Freesurfer] question abt flattening in freesurfer

[Ritobrato Datta]

Hi All,
My name is Ritobrato Datta and I am a post-doc at PENN. I have just started 
learning Freesurfer. 
I am trying to create occipital flatmap in freesurfer using the command 
mris_flatten. I followed the commands as described but am getting the following 
error. 
I created the lh.occip.patch.3d and its there in the surf directory. 

Following is the error-
-
mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat
using write iterations = 0
sampling 7 neighbors out to a distance of 20 mm
reading patch lh.occip.patch.3d with 1919246708 vertices (1096499.4% of total)
MRISreadPatch: bad vertex # (1701060705) found in patch file
No such file or directory
-
Any suggestions will be highly appreciated.
Thanks much

Ri

Ritobrato Datta, Ph.D.
Post Doctoral Fellow
Department of Neurology
University of Pennsylvania School of Medicine
3rd Floor Gates Building
3400 Spruce St. 
Philadelphia
Pa 19104


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