Re: [Freesurfer] Geometric distortion

[Martin Juneja]

External Email - Use Caution

Thank you Matthew for your reply.

I just ran recon-all to get cortical thickness, area and volume values for
specific ROIs using the steps here:
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
and correlated the morphometric values with behavioral data.
I am not sure how can I address reviewer's comment.

Any help would be really appreciated.

On Mon, May 13, 2019 at 5:41 PM Glasser, Matthew  wrote:

> External Email - Use Caution
>
> There are different kinds of geometric distortion that affect your data to
> differing extents.  What kind of MRI data was in your study?
>
> Matt.
>
>
>
> *From: * on behalf of Martin
> Juneja 
> *Reply-To: *Freesurfer support list 
> *Date: *Monday, May 13, 2019 at 6:53 PM
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] Geometric distortion
>
>
>
> *External Email - Use Caution*
>
> Hi experts,
>
>
>
> I have following question from one of the reviewers regarding recon-all
> pipeline:
>
> *"Was geometric distortion corrected? If not, this should be discussed or
> mentioned in the study limitation."*
>
> I was wondering if the reviewer is referring to following step in the
> recon-all pipeline. Could you please help me in addressing this concern by
> the reviewer?
>
>
>
> Thanks.
>
> MJ
> Cortical Parcellation (-cortparc, -cortparc2)
> Assigns a neuroanatomical label to each location on the cortical surface.
> Incorporates both geometric information derived from the cortical model
> (sulcus and curvature), and neuroanatomical convention. Calls
> mris_ca_label. -cortparc creates label/?h.aparc.annot, and -cortparc2
> creates /label/?h.aparc.a2005s.annot.
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] check FS to native registration in freeview

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

you have to use the output of mri_label2vol in the freeview command

On 5/13/2019 5:02 PM, Sam W. wrote:

External Email - Use Caution

Hi,

After bbregister, I ran mri_label2vol to convert a segmentation file to native 
functional space

mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat --subject s01 --o 
aseg-in-func.nii --temp example_func.nii

Now I would like to check how well the example_func and aseg file align.

I tried this
freeview -v s01/example_func.nii s01/aseg.mgz:colormap=lut:reg=reg.dat
but it does not result in a good alignment

Best regards,
Sam




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

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

Re: [Freesurfer] Geometric distortion

[Glasser, Matthew]

External Email - Use Caution

There are different kinds of geometric distortion that affect your data to 
differing extents.  What kind of MRI data was in your study?

Matt.

From:  on behalf of Martin Juneja 

Reply-To: Freesurfer support list 
Date: Monday, May 13, 2019 at 6:53 PM
To: Freesurfer support list 
Subject: [Freesurfer] Geometric distortion


External Email - Use Caution
Hi experts,

I have following question from one of the reviewers regarding recon-all 
pipeline:
"Was geometric distortion corrected? If not, this should be discussed or 
mentioned in the study limitation."
I was wondering if the reviewer is referring to following step in the recon-all 
pipeline. Could you please help me in addressing this concern by the reviewer?

Thanks.
MJ
Cortical Parcellation (-cortparc, -cortparc2)
Assigns a neuroanatomical label to each location on the cortical surface. 
Incorporates both geometric information derived from the cortical model (sulcus 
and curvature), and neuroanatomical convention. Calls mris_ca_label. -cortparc 
creates label/?h.aparc.annot, and -cortparc2 creates 
/label/?h.aparc.a2005s.annot.


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Geometric distortion

[Martin Juneja]

External Email - Use Caution

Hi experts,

I have following question from one of the reviewers regarding recon-all
pipeline:
*"Was geometric distortion corrected? If not, this should be discussed or
mentioned in the study limitation."*
I was wondering if the reviewer is referring to following step in the
recon-all pipeline. Could you please help me in addressing this concern by
the reviewer?

Thanks.
MJ
Cortical Parcellation (-cortparc, -cortparc2)
Assigns a neuroanatomical label to each location on the cortical surface.
Incorporates both geometric information derived from the cortical model
(sulcus and curvature), and neuroanatomical convention. Calls
mris_ca_label. -cortparc creates label/?h.aparc.annot, and -cortparc2
creates /label/?h.aparc.a2005s.annot.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] check FS to native registration in freeview

[Sam W.]

External Email - Use Caution

Hi,

After bbregister, I ran mri_label2vol to convert a segmentation file to
native functional space

mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat --subject s01 --o
aseg-in-func.nii --temp example_func.nii

Now I would like to check how well the example_func and aseg file align.

I tried this
freeview -v s01/example_func.nii s01/aseg.mgz:colormap=lut:reg=reg.dat
but it does not result in a good alignment

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

[Freesurfer] Research Assistant Position at Massachusetts Eye and Ear/Harvard Medical School in Boston, MA

[Bailin, Emma]

The Laboratory for Visual Neuroplasticity at the Massachusetts Eye and Ear 
Infirmary (Harvard Medical School), located in Boston, MA is seeking a 
full-time research assistant to start between July and September 2019. 
Candidates who would be able to commit to the position for a minimum of two 
years would be strongly preferred. Led by Dr. Lotfi Merabet, the computational 
neuroscience lab studies how the brain adapts to blindness and visual 
impairment. Major research focuses include brain imaging technologies 
(including MRI and EEG) to investigate structural and functional 
neuroplasticity as well as development of behavioral stimuli (virtual reality) 
for research into cerebral and ocular visual impairments. Detailed information 
about the lab can be found at http://scholar.harvard.edu/merabetlab.

Responsibilities: The research assistant will assist with behavioral and MRI 
data management and analysis (~75% of the time), conduct experiments (~10%), 
and perform various administrative tasks (~15%).

Qualifications: Ideal candidates will have a bachelor's degree or equivalent in 
neuroscience, computer science, or psychology. An interest in working with 
people with disabilities would be highly desirable. Some research experience in 
a neuroscience and or an experimental psychology lab would be good, but not 
required. Strong organizational and communication skills and attention to 
detail are an important must. The candidate should be self-motivated and able 
to solve problems independently while also being comfortable working with 
others. Applicants with a background in programming (e.g. Unix, Python, 
MATLAB), statistical analysis software (e.g. R, SPSS, Stata) and/or 
neuroimaging software (e.g. FreeSurfer, FSL, SPM, etc.) are strongly encouraged 
to apply.

To Apply: Please send a CV and a cover letter to Emma Bailin 
(emma_bai...@meei.harvard.edu), with the 
subject line "Research Assistant position application". The letter should 
describe your research experience (if you have any), interests and include why 
you think you would be a good fit for the lab. Please also include the name and 
contact information of two references. Applications will be reviewed on rolling 
basis until the position has been filled.


Emma Bailin
Research Coordinator
Laboratory for Visual Neuroplasticity
Schepens Eye Research Institute
Mass. Eye and Ear Infirmary
Harvard Medical School
emma_bai...@meei.harvard.edu



Mass. Eye and Ear Confidentiality Notice: This e-mail and any files transmitted 
with it are confidential and are intended solely for the use of the 
individual(s) addressed in the message above. This communication may contain 
sensitive or confidential information. If you are not an intended recipient, 
dissemination, forwarding, printing, or copying of this e-mail is strictly 
prohibited. If you believe you have received this e-mail in error and the email 
contains patient information, please contact the Mass. Eye and Ear Compliance 
Line at (800) 856-1983. If the e-mail was sent to you in error but does not 
contain patient information, please contact the sender and delete the e-mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] MP2RAGE recon using Siemens Terra 7T scanner

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

I would use the high res stream I made for the HCP
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/


On 5/13/19 4:23 PM, Fuller-Deets, Josh (NIH/NEI) [C] wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer users,
>
>
> we have a new Terra 7T scanner and I'm having issues collecting a 
> clean MP2RAGE scan and subsequently reconstructing it. Does anyone 
> with experience with this scanner have any suggestions about 
> modifications to the standard Siemens provided sequence? 
> Alternatively, does anyone have any suggestions for any expert 
> file/input settings for recon-all other than what is in the high field 
> recon and submillimeter recon help pages?
>
>
> Thanks for your time,
>
>
> Joshua Fuller-Deets
>
> Computer Systems Analyst [C]
>
> Laboratory of Sensorimotor Research
>
> National Eye Institute
>
> 49 Convent Drive, Rm. 2B75
>
> Phone: 301-496-3708
>
> Fax: 301-402-0511
>
> Email: josh.fuller-de...@nih.gov
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

[Freesurfer] MP2RAGE recon using Siemens Terra 7T scanner

[Fuller-Deets, Josh (NIH/NEI) [C]]

External Email - Use Caution

Hi Freesurfer users,


we have a new Terra 7T scanner and I'm having issues collecting a clean MP2RAGE 
scan and subsequently reconstructing it. Does anyone with experience with this 
scanner have any suggestions about modifications to the standard Siemens 
provided sequence? Alternatively, does anyone have any suggestions for any 
expert file/input settings for recon-all other than what is in the high field 
recon and submillimeter recon help pages?


Thanks for your time,


Joshua Fuller-Deets

Computer Systems Analyst [C]

Laboratory of Sensorimotor Research

National Eye Institute

49 Convent Drive, Rm. 2B75

Phone: 301-496-3708

Fax: 301-402-0511

Email: josh.fuller-de...@nih.gov
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Spatial smoothing kernel in fsfast

[Zhi Li]

External Email - Use Caution

Dear Freesurfer experts.

Now I am using preproc-sess to preprocess functional MRI data. I would like
to smooth the data first and then resample them into the standard space.
Hence I run 'preproc-sess -s sub001 -fsd func -stc odd -fwhm 0 -per-run'
first, and then 'spatialsmooth-sess -s sub001 -fsd func -i fmcpr.odd -o
fmcpr.odd.sm5 -fwhm 5', finally 'preproc-sess -s sub001 -fsd func -stc odd
-surface fsaverage lhrh -mni305 -fwhm 0 -per-run' (I have already renamed
the stem of smoothed file from fmcpr.odd.sm5 to fmcpr.odd). However, the
preprocessed data 'fmcpr.odd.sm0.mni305.2mm.nii.gz' contains both cortical
and subcortical data. If I use '-fwhm 1' this file only contains the
subcortical area. May I know why and how to fix it?

About each stage embedded in 'preproc-sess', if I would like replace one
stage with other software/algorithms, can I just change the name of the
generated file by other software/algorithms to the name of file in this
stage of 'prepoc-sess', and them rerun 'preproc-sess' while keep the flag
'-update' on? For example, if I would like to use FSL/SPM to register the
functional image to structural data, can I just rename the mat-file which
describes the affine registration generated by FSL/SPM to
'register.dof6.mat'?

Looking forward to your kind suggestions.

Thanks and best wishes,

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

Re: [Freesurfer] spatial scale bar question

[Nasiriavanaki, Zahra]

Great!
Thanks

> On May 13, 2019, at 9:56 AM, Bruce Fischl  wrote:
> 
> Hi Mona
> 
> sure. As I said it is a bit more complicated than it seems. Ruopeng will post 
> a note when something usable is in the dev version
> 
> Bruce
> 
> 
> On Mon, 13 May 2019, Nasiriavanaki, Zahra wrote:
> 
>> Yes Bruce.
>> It doesn't work.
>> I appreciate if you could let me know when you had any updates on it.
>> Thanks
>> Mona
>> ___
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of
>> Bruce Fischl 
>> Sent: Friday, May 10, 2019 6:15:05 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] spatial scale bar question  
>> I don't think it currently works in 3D mode as it is not trivial due to
>> perspective transforms. Ruopeng is trying some things
>> On Fri, 10 May 2019,
>> Greve, Douglas N.,Ph.D. wrote:
>> > here is a pick of it
>> > https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif
>> [fv.colorbar.gif]
>> >
>> >
>> > On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
>> >
>> >   Thanks for your reply.
>> >
>> >   I have overlaid the significance map on an inflated brain, and I 
>> > don't see the scale
>> >   bar icon anywhere.
>> >
>> >   tksurferfv fsaverage lh inflated -ov sig.nii.gz
>> >
>> >
>> >__
>> _
>> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> >  on
>> > behalf of Greve, Douglas N.,Ph.D. 
>> > Sent: Friday, May 10, 2019 3:27:15 PM
>> > To: freesurfer@nmr.mgh.harvard.edu
>> > Subject: Re: [Freesurfer] spatial scale bar question  
>> > In freeview, it is just an icon above the image window. Click on it and it 
>> > should give you a
>> > scale bar
>> >
>> > On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
>> >
>> >   Dear Freesurfers 
>> >
>> >   Hi
>> >
>> >
>> >   I am trying to add a spatial scale bar to my cortical maps in 
>> > tksurfer. However,
>> >   as it's mentioned in Freesurfer forum before, the scale bar in 
>> > tksurfer shrinks
>> >   when you zoom in the brain.
>> >
>> >   I couldn't find a scale bar option in Freeview neither.
>> >
>> >   I appreciate if you could let me know how to get a scale bar.
>> >
>> >
>> >   Thanks
>> >
>> >   Mona
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> >
>> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] spatial scale bar question

[Bruce Fischl]

Hi Mona

sure. As I said it is a bit more complicated than it seems. Ruopeng will 
post a note when something usable is in the dev version


Bruce


On Mon, 13 May 
2019, Nasiriavanaki, Zahra wrote:




Yes Bruce.

It doesn't work.

I appreciate if you could let me know when you had any updates on it.


Thanks

Mona

___
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of
Bruce Fischl 
Sent: Friday, May 10, 2019 6:15:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] spatial scale bar question  
I don't think it currently works in 3D mode as it is not trivial due to
perspective transforms. Ruopeng is trying some things
On Fri, 10 May 2019,
Greve, Douglas N.,Ph.D. wrote:

> here is a pick of it
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif

[fv.colorbar.gif]


>
>
> On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
>
>   Thanks for your reply.
>
>   I have overlaid the significance map on an inflated brain, and I don't 
see the scale
>   bar icon anywhere.
>
>   tksurferfv fsaverage lh inflated -ov sig.nii.gz
>
>
>__
_
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on
> behalf of Greve, Douglas N.,Ph.D. 
> Sent: Friday, May 10, 2019 3:27:15 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] spatial scale bar question  
> In freeview, it is just an icon above the image window. Click on it and it 
should give you a
> scale bar
>
> On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
>
>   Dear Freesurfers 
>
>   Hi
>
>
>   I am trying to add a spatial scale bar to my cortical maps in tksurfer. 
However,
>   as it's mentioned in Freesurfer forum before, the scale bar in tksurfer 
shrinks
>   when you zoom in the brain.
>
>   I couldn't find a scale bar option in Freeview neither.
>
>   I appreciate if you could let me know how to get a scale bar.
>
>
>   Thanks
>
>   Mona
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>

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

Re: [Freesurfer] spatial scale bar question

[Nasiriavanaki, Zahra]

Yes Bruce.

It doesn't work.

I appreciate if you could let me know when you had any updates on it.


Thanks

Mona


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

Sent: Friday, May 10, 2019 6:15:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] spatial scale bar question

I don't think it currently works in 3D mode as it is not trivial due to
perspective transforms. Ruopeng is trying some things
On Fri, 10 May 2019,
Greve, Douglas N.,Ph.D. wrote:

> here is a pick of it
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif

[https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif]

>
>
> On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
>
>   Thanks for your reply.
>
>   I have overlaid the significance map on an inflated brain, and I don't 
> see the scale
>   bar icon anywhere.
>
>   tksurferfv fsaverage lh inflated -ov sig.nii.gz
>
>
> ___
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on
> behalf of Greve, Douglas N.,Ph.D. 
> Sent: Friday, May 10, 2019 3:27:15 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] spatial scale bar question
> In freeview, it is just an icon above the image window. Click on it and it 
> should give you a
> scale bar
>
> On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
>
>   Dear Freesurfers
>
>   Hi
>
>
>   I am trying to add a spatial scale bar to my cortical maps in tksurfer. 
> However,
>   as it's mentioned in Freesurfer forum before, the scale bar in tksurfer 
> shrinks
>   when you zoom in the brain.
>
>   I couldn't find a scale bar option in Freeview neither.
>
>   I appreciate if you could let me know how to get a scale bar.
>
>
>   Thanks
>
>   Mona
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] How can I visualize cortical thickness data on a brain template?

[Bruce Fischl]

Hi Alberto

yes, you should be able to. Do you have the individual datasets or some 
type of average?

cheers
Bruce


On Mon, 13 May 2019, albertotricker wrote:

>External Email - Use Caution
>
> Hello FreeSurfer technical staff
>
> I hava a data set provided by ADNI initiative, which is formed by a set
> of pre-processed T1-weighted MRI using FreeSurfer. The feature space
> consists of cortical thickness and subcortical volumes.
>
> Well, I want to visualice the cortical thickness features on a brain
> template to obtain something like this:
>
> https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image%20to%20zoom&p=PMC3&id=2741580_gr4.jpg
>
> It is possible to do that with FreeSurfer, or I have to use other tool?
> I am sorry if the question if not complete, please tell me if you need
> more information.
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] tractstats2table error

[Daniel Callow]

External Email - Use Caution

Sorry, I realized I used the pathstats.byvoxel.txt instead of
pathstats.overall.txt.

Attached is the correct .txt file and the new error I get from the python
script called by tractstats2table

pathstats.overall.txt

Parsing the .stats files

Building the table..

Traceback (most recent call last):

  File "/Applications/freesurfer_dev/bin/tractstats2table", line 368, in


r1c1, rows, columns, table = sanitize_table(options, pretable)

  File "/Applications/freesurfer_dev/bin/tractstats2table", line 260, in
sanitize_table

if not 1 == len(pthwyset.keys()):

  File "/Applications/freesurfer_dev/bin/datastruct_utils.py", line 281, in
keys

return self.__ksl[:]

TypeError: 'dict_keys' object is not subscriptable


*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


On Mon, May 13, 2019 at 9:04 AM Daniel Callow  wrote:

> Hello,
>
> I just ran trac-all on my data and am trying to use tractstats2table to
> run some tract-based group level analysis.
>
> I have created a text file with the full paths to each conditions stats
> file (attached below and tried to run the following command
>
> tractstats2table --load-pathstats-from-file
> /Volumes/DANIEL/trac/stats_info/stats_rh.unc.txt --overall --tablefile
> /Volumes/DANIEL/trac/stats_info/rh.unc.All.table
>
>
> However, I get the following error message.
>
>
> Parsing the .stats files
>
> Traceback (most recent call last):
>
>   File "/Applications/freesurfer_dev/bin/tractstats2table", line 347, in
> 
>
> pathway_subj, measure_value_map = parsed.parse()
>
>   File "/Applications/freesurfer_dev/bin/fsutils.py", line 288, in parse
>
> val = float(strlist[1])
>
> ValueError: could not convert string to float: 'y'
>
>
> Could someone please provide me some guidance on how to troubleshoot this?
>
>
> *Daniel Callow*
> *PhD Student, Neuroscience and Cognitive Science*
> Exercise for Brain Health Lab
> University of Maryland, College Park
> *ddcc2...@gmail.com *
> 443-254-6298
>
/Volumes/DANIEL/trac/Ex.AES101.long.base_AES101/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Rest.AES101.long.base_AES101/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Ex.AES102.long.base_AES102/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Rest.AES102.long.base_AES102/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Ex.AES104.long.base_AES104/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Rest.AES104.long.base_AES104/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Ex.AES107.long.base_AES107/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Rest.AES107.long.base_AES107/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Ex.AES108.long.base_AES108/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Rest.AES108.long.base_AES108/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Ex.AES109.long.base_AES109/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Rest.AES109.long.base_AES109/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Ex.AES110.long.base_AES110/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Rest.AES110.long.base_AES110/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Ex.AES111.long.base_AES111/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Rest.AES111.long.base_AES111/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Ex.AES113.long.base_AES113/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Rest.AES113.long.base_AES113/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Ex.AES114.long.base_AES114/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Rest.AES114.long.base_AES114/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Ex.AES115.long.base_AES115/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Rest.AES115.long.base_AES115/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Ex.AES116.long.base_AES116/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Rest.AES116.long.base_AES116/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Ex.AES117.long.base_AES117/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Rest.AES117.long.base_AES117/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Ex.AES118.long.base_AES118/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Rest.AES118.long.base_AES118/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
/Volumes/DANIEL/trac/Ex.AES119.long.ba

[Freesurfer] tractstats2table error

[Daniel Callow]

External Email - Use Caution

Hello,

I just ran trac-all on my data and am trying to use tractstats2table to run
some tract-based group level analysis.

I have created a text file with the full paths to each conditions stats
file (attached below and tried to run the following command

tractstats2table --load-pathstats-from-file
/Volumes/DANIEL/trac/stats_info/stats_rh.unc.txt --overall --tablefile
/Volumes/DANIEL/trac/stats_info/rh.unc.All.table


However, I get the following error message.


Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer_dev/bin/tractstats2table", line 347, in


pathway_subj, measure_value_map = parsed.parse()

  File "/Applications/freesurfer_dev/bin/fsutils.py", line 288, in parse

val = float(strlist[1])

ValueError: could not convert string to float: 'y'


Could someone please provide me some guidance on how to troubleshoot this?


*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
/Volumes/DANIEL/trac/Ex.AES101.long.base_AES101/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES101.long.base_AES101/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES102.long.base_AES102/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES102.long.base_AES102/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES104.long.base_AES104/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES104.long.base_AES104/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES107.long.base_AES107/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES107.long.base_AES107/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES108.long.base_AES108/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES108.long.base_AES108/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES109.long.base_AES109/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES109.long.base_AES109/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES110.long.base_AES110/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES110.long.base_AES110/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES111.long.base_AES111/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES111.long.base_AES111/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES113.long.base_AES113/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES113.long.base_AES113/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES114.long.base_AES114/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES114.long.base_AES114/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES115.long.base_AES115/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES115.long.base_AES115/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES116.long.base_AES116/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES116.long.base_AES116/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES117.long.base_AES117/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES117.long.base_AES117/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES118.long.base_AES118/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES118.long.base_AES118/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES119.long.base_AES119/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES119.long.base_AES119/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES120.long.base_AES120/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES120.long.base_AES120/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES121.long.base_AES121/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES121.long.base_AES121/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES122.long.base_AES122/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES122.long.base_AES122/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES123.long.base_AES123/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Rest.AES123.long.base_AES123/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt
/Volumes/DANIEL/trac/Ex.AES124.long.base_AES124/dpath/

Re: [Freesurfer] Longitudinal processing

[falk.luesebr...@med.ovgu.de]

External Email - Use Caution

Hi Martin,

thanks for your quick reply and the clarification regarding the output.

I have processed the 1 and 0.8 mm separately, so one base for each subject and 
resolution - no mixing has been conducted! :)

Actually, I want to look into changes due to hydration and other biological 
effects, e.g. due to hormone status. However, this is just a preliminary 
assessment of the variance in general (and getting to know the processing 
pipeline) as no meta data was acquired to correlate the measures against. 

Best,
Falk

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Martin Reuter
Gesendet: Montag, 13. Mai 2019 12:56
An: Freesurfer support list 
Betreff: Re: [Freesurfer] Longitudinal processing

Hi Falk, 

yes, the output of long_mris_slopes and long_stats_slopes is in percent
(100 * rate / value_of_fit_at_mid_time). 

Also running 1mm data is different (as you know :-) from .8 so maybe you would 
analyze both separately, e.g. creating one base on 1mm time points and another 
on the .8mm ? 

If you re-scan in short time interals (and if these are young and healthy, then 
even for mid to long intervals), you would not expect anatomical aging effects. 
Then the variance is probably mainly acquisition noise (e.g. induced by motion 
etc, see eg
https://www.ncbi.nlm.nih.gov/pubmed/25498430) plus some processing noise 
(different surface placement etc). Maybe there are also hydration effects (see 
https://www.ncbi.nlm.nih.gov/pubmed/26381562 ). 

Best, Martin


On Thu, 2019-05-09 at 09:51 +, falk.luesebr...@med.ovgu.de wrote:
> External Email - Use Caution
> Dear all,
>  
> I’m a beginner in using the longitudinal processing pipeline (as well 
> as statistical analysis) and it would be great to get some insights or 
> hints to analyze my data.
>  
> I have a dataset consisting of 11 subjects each acquired at 7 
> different time points with an isotropic resolution of 1 and 0.8 mm at 
> 3T using a 64-channel head coil. Using that dataset I want to 
> investigate short term differences in e.g. cortical thickness with the 
> goal to assess the degree of biological variance during that time 
> period.
>  
> I have plotted the mean cortical thickness of each time point of every 
> subject (using lme_timePlot and lme_lowessPlot) showing a somewhat 
> random distribution across time and from my perspective fairly high 
> standard deviation. I wanted to have a look at the individual percent 
> change by overlaying the symmetric percent change on fsaverage, but 
> wasn’t quite sure of the scale. Is it in percent?
> So in case I set the scale bar between 1 and 5, the color relates to
> 1 to 5 percent?
>  
> What other ways would make sense to have a look at? I definitely 
> cannot compare groups, as there is just one. The days and time of 
> acquistion are rather randomly choosen, so I potentially cannot use 
> either as a covariate.
>  
> Best,
> Falk
>  
> ...
>  
> 
> University Clinic for Neurology
>  
> Otto-von-Guericke-university Magdeburg Medical faculty Leipziger Str. 
> 44
> 39120 Magdeburg
>  
> Phone +49-391-6117-512
> 
> falk.luesebr...@med.ovgu.de
> http://www.kneu.ovgu.de/kneu.html
>  
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

[Freesurfer] mni152reg ends with (ERROR: flirt)

[vin rasa]

External Email - Use Caution

Dear Freesurfer Experts!

The idea is to transform freesurfer output in to the MNI 1mm space using
following command:

mni152reg --s subject_id --1

But mni152reg crashes with following error:

flirt.newdefault.20080811.sch
terminate called after throwing an instance of 'NEWMAT::SingularException'
ERROR: flirt

Your help is appreciated!

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

[Freesurfer] mri_vol2surf for functional 4D BOLD data only mapping 1 frame

[Robert Austin Bruce Benn]

External Email - Use Caution

Hi There,

I’m currently trying to run mri_vol2surf on some animal data and surfaces I’ve 
been working with.
I’m having a bit of a problem with the command mri_vol2surf.
I seem to be able to project my functional volume to my surface, however I’m 
currently only projecting the first volume of my functional time series onto 
the surface.
I realize the default option for frame is the first volume if output is set to 
a paint file, however I’m not trying to do that.

Ideally I’d like to project all the volumes for later connectivity analysis.

The command and terminal output are as  follows:

mri_vol2surf --mov rest.acp/filtered_func_data_clean.nii.gz --reg 
rest.acp/reg/example_func2FS.dat --surf white  --projfrac 0.5 --hemi lh --o 
rest.acp/test.func.mgh

srcvol = rest.acp/filtered_func_data_clean.nii.gz
srcreg = rest.acp/reg/example_func2FS.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
INFO: This REGISTER_DAT transform is valid only for volumes between  COR types 
with c_(r,a,s) = 0.
Input reg is register.dat
 original matrix ---
 0.99985  -0.01410   0.01053   2.56773;
 0.01269   0.99230   0.12321  -20.18632;
-0.01219  -0.12306   0.99232   0.65897;
 0.0   0.0   0.0   1.0;
 original matrix ---
Reading surface /Volumes/brain/PCP_func/5489/anat/surf/lh.white
Done reading source surface
Reading thickness /Volumes/brain/PCP_func/5489/anat/surf/lh.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 = 2868
Writing to rest.acp/test.func.nii
Dim: 19181 1 1

The actual functional volumes has 300 volumes, so I feel like I should be 
getting Dim: 19181 1 1 300 ?

any advice?

thanks,

austin



*** AVISO LEGAL ***
Este mensaje va dirigido, de manera exclusiva, a su destinatario y
contiene información confidencial y sujeta al secreto profesional,
cuya divulgación no está permitida por la ley. En caso de haber
recibido este mensaje por error, le rogamos que, de forma inmediata,
nos lo comunique mediante correo electrónico remitido a nuestra
atención o a través del teléfono (+34 914531200) y proceda a su
eliminación, así como a la de cualquier documento adjunto al mismo.
Asimismo, le comunicamos que la distribución, copia o utilización de
este mensaje, o de cualquier documento adjunto al mismo, cualquiera
que fuera su finalidad, están prohibidas por la ley. Le informamos,
como destinatario de este mensaje, que el correo electrónico y las
comunicaciones por medio de Internet no permiten asegurar ni
garantizar la confidencialidad de los mensajes transmitidos, así como
tampoco su integridad o su correcta recepción, por lo que el CNIC no
asume responsabilidad alguna por tales circunstancias. Si no
consintiese la utilización del correo electrónico o de las
comunicaciones vía Internet le rogamos nos lo comunique y ponga en
nuestro conocimiento de manera inmediata.

*** LEGAL NOTICE **
This message is intended exclusively for the person to whom it is
addressed and contains privileged and confidential information
protected from disclosure by law. If you are not the addressee
indicated in this message, you should immediately delete it and any
attachments and notify the sender by reply e-mail or by phone
(+34 914531200). In such case, you are hereby notified that any
dissemination, distribution, copying or use of this message or any
attachments, for any purpose, is strictly prohibited by law. We
hereby inform you, as addressee of this message, that e-mail and
Internet do not guarantee the confidentiality, nor the completeness
or proper reception of the messages sent and, thus, CNIC does not
assume any liability for those circumstances. Should you not agree
to the use of e-mail or to communications via Internet, you are
kindly requested to notify us immediately.___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Longitudinal processing

[Martin Reuter]

Hi Falk, 

yes, the output of long_mris_slopes and long_stats_slopes is in percent
(100 * rate / value_of_fit_at_mid_time). 

Also running 1mm data is different (as you know :-) from .8 so maybe
you would analyze both separately, e.g. creating one base on 1mm time
points and another on the .8mm ? 

If you re-scan in short time interals (and if these are young and
healthy, then even for mid to long intervals), you would not expect
anatomical aging effects. Then the variance is probably mainly
acquisition noise (e.g. induced by motion etc, see eg 
https://www.ncbi.nlm.nih.gov/pubmed/25498430) plus some processing
noise (different surface placement etc). Maybe there are also hydration
effects (see https://www.ncbi.nlm.nih.gov/pubmed/26381562 ). 

Best, Martin


On Thu, 2019-05-09 at 09:51 +, falk.luesebr...@med.ovgu.de wrote:
> External Email - Use Caution
> Dear all,
>  
> I’m a beginner in using the longitudinal processing pipeline (as well
> as statistical analysis) and it would be great to get some insights
> or hints to analyze my data.
>  
> I have a dataset consisting of 11 subjects each acquired at 7
> different time points with an isotropic resolution of 1 and 0.8 mm at
> 3T using a 64-channel head coil. Using that dataset I want to
> investigate short term differences in e.g. cortical thickness with
> the goal to assess the degree of biological variance during that time
> period.
>  
> I have plotted the mean cortical thickness of each time point of
> every subject (using lme_timePlot and lme_lowessPlot) showing a
> somewhat random distribution across time and from my perspective
> fairly high standard deviation. I wanted to have a look at the
> individual percent change by overlaying the symmetric percent change
> on fsaverage, but wasn’t quite sure of the scale. Is it in percent?
> So in case I set the scale bar between 1 and 5, the color relates to
> 1 to 5 percent?
>  
> What other ways would make sense to have a look at? I definitely
> cannot compare groups, as there is just one. The days and time of
> acquistion are rather randomly choosen, so I potentially cannot use
> either as a covariate.  
>  
> Best,
> Falk
>  
> ...
>  
> 
> University Clinic for Neurology
>  
> Otto-von-Guericke-university Magdeburg
> Medical faculty
> Leipziger Str. 44
> 39120 Magdeburg
>  
> Phone +49-391-6117-512
> 
> falk.luesebr...@med.ovgu.de
> http://www.kneu.ovgu.de/kneu.html
>  
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Re: [Freesurfer] Longitudinal Gray/white Contrast Measure

[Martin Reuter]

Hi William, 

you can use freesurfer's pctsurfcon to compute the gray/white contrast
on the longitudinal directories. This will produce a surface overlay
at: tp.long.base/surf/?h.w-g.pct.mgh 

I don't think the long_mris_slopes script can deal with those files
directly, so you have two options:

- take a look at that script and run the same commands manually for the
w-g.pct.mgh files

- convert the pct.mgh  files to thickness format, rename volume to
something else, rename the w-g.pct to volume , run long_mris_slopes and
rename everything back. 

Best, Martin



On Mon, 2019-05-06 at 16:41 -0700, WON JONG CHWA wrote:
> External Email - Use Caution
> Dear FreeSurfer experts,
> 
> I am currently running a longitudinal analysis in FreeSurfer v5.3 to
> look at changes in volume and gray/white contrast. I ran all the
> processing steps and used this command below to look at results for
> volume:
> 
> long_mris_slopes --qdec ./qdec/qdec.table.dat --meas volume --hemi lh
> --do-label --do-rate --time years --qcache fsaverage --sd
> $SUBJECTS_DIR
> 
> We also would like to look at change in gray-white matter intensity
> ratio over time (between 2 timepoints) as well, but there is no
> separate measure defined for it. I was wondering what we can do to
> calculate this.
> 
> Thank you.
> William
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

[Freesurfer] How can I visualize cortical thickness data on a brain template?

[albertotricker]

External Email - Use Caution

Hello FreeSurfer technical staff

I hava a data set provided by ADNI initiative, which is formed by a set 
of pre-processed T1-weighted MRI using FreeSurfer. The feature space 
consists of cortical thickness and subcortical volumes.

Well, I want to visualice the cortical thickness features on a brain 
template to obtain something like this:

https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image%20to%20zoom&p=PMC3&id=2741580_gr4.jpg

It is possible to do that with FreeSurfer, or I have to use other tool? 
I am sorry if the question if not complete, please tell me if you need 
more information.


-- 
1/8/1996
 Huétor Tájar

Alberto Martín Martín
  _Estudiante de Ingeniería Electrónica Industrial_

UGR

_Ingeniero en proceso (de volverse loco)_

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