[Freesurfer] KWWidgets

[Melvin Robinson]

A FreeSurfer build from source requires KWWidgets, but it has been deprecated 
for 10 years.  What does Freesurfer use this code for?
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Re: [Freesurfer] Creating ROI on the functional map

[Sarah Cole]

It doesn't work on tksurfer. But it's ok.

So Doug, is this the latest tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview
for FS-FAST and creating functional ROI?

More specifically, do I need to use "mri_vol2surf" to get the activation on
the surface?

This was not in the other tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastFirstLevel


Thanks

On Mon, Feb 26, 2018 at 3:28 PM, Douglas N Greve 
wrote:

> I think it should work; We are not using tksurfer any more (freeview
> instead), but I think it should still work
>
>
> On 02/23/2018 05:16 PM, Sarah Cole wrote:
> > Hi,
> >
> > I was wondering if this method is still applicable in version 6
> > https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs
> >
> >
> > I cannot seem to find any of the options for creating an ROI.
> >
> > Thank you,
> >
> > S
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
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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
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>
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Re: [Freesurfer] aseg and aparcstats2table on longitudinal data

[Douglas N Greve]

I don't know about #1 (I think not). For #2 you shold use the subject 
names from the longitudinal analysis


On 02/26/2018 11:39 AM, Lisa Delalande wrote:
> Hi FreeSurfer experts,
>
> I would like to use the asegstats2table and the aparcstats2table 
> commands on my longitudinal data, that have been processing following 
> the longitudinal pipeline (recon-all -cross, - base and finally 
> -long). And I have two questions :
>
> 1) Am I obliged to do the long_stats_slopes --qdec 
> ./qdec/longi_presentacio.qdec.table.dat --stats aseg.stats --meas 
> volume --do-avg --do-rate --do-pc1 --time months command before using 
> the aseg/aparc commands ?
>
> 2) And I would like to know which subjectsID I have to choose for the 
> command line, example :
> asegstats2table --subjects *001_tp1 002_tp1*...etc. (cross)? OR 
> *template_001 template_002*...etc (base)? OR 
> *001_tp1.long.template_001 002_tp1.long.template_002*...etc (long)?
> Knowing that it's for a comparison test-retest (microlongitudinal : 1 
> month).
>
>
> Thanks you for your precious help,
> Best regards,
>
> Lisa
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] questions about the segamentation volume

[Douglas N Greve]

You should check the accuracy of the segmentations in a few of the 
outlier subjects


On 02/26/2018 03:18 PM, Ting Li wrote:
> Hi FreeSurfer Expert,
>
> I followed the Anatomical ROI analysis tutorial and make a 
> aseg.vol.table for the 40 subjects. However, the segment volume can 
> various a lot in different subjects, such as Left-Lateral-Ventricle, 
> Left-Inf-Lat-Vent. I attached a screenshot. Thanks for your response.
>
> Best wishes,
> Ting
>
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] FSGD and Contrast to determine the effect of age on performance

[Douglas N Greve]

You would keep both Perform and Age in addition to adding Perform*Age. I 
would first use DODS to test for a difference between groups in the 
Perform*Age variable [0 0 0 0 0 0 1 -1]. If there are no differences, 
then use DOSS to test for an effect of Perform*Age [0 0 0 0 1].


On 02/26/2018 04:40 PM, Martin Juneja wrote:
> Thanks much Dough for your reply.
>
> So if I add another column Performance*Age (after removing the mean of 
> each) in my fsgd file (and remove individual columns for Performance 
> and age), could you please tell what will be the contrast matrix 
> (after only Gender as a covariate) in that case i.e. for following fsgd:
>
> Class Male
> Class Female
> Variables *Perform*Age*
> Input S1 Male 180
> Input S2 Female 167
>
> Thanks.
>
> On Mon, Feb 26, 2018 at 2:31 PM, Douglas N Greve 
> > wrote:
>
>
>
> On 02/24/2018 12:00 AM, Martin Juneja wrote:
> > Hi experts,
> >
> > I am not sure if this has already been addressed in FS discussion.
> >
> > If my fsgd file looks like following:
> >
> > Class Male
> > Class Female
> > Variables Performance Age
> > Input S1 Male 181 25
> > Input S2 Female 167 23
> > 
> > 
> >
> > I understand that the contrast matrix *[**0 0 1 -1 0 0]* represents
> > whether there is a difference between the group
> > (male/female)-performance slopesregressing out the effect of age. In
> > other words, this matrix calculates whether two slopes i.e. one for
> > males: thickness-performance slope and second for females:
> > thickness-performance slope - are significantly different after
> > regressing out the effect of age.
> >
> > My questions are following:
> >
> > (1) Is my above interpretation of contrast matrix*[**00 1 -1 0
> > 0]* correct?
> Yes
> > (2) If my interpretation is correct, then I was wondering what will be
> > the contrast matrix if *I want to check whether there is
> **significant
> > effect of age on e.g. thickness-performance slopes after regressing
> > out the effect of gender.* And what will be the corresponding fsgd
> > file for that, any changes in that?
> This is an interaction between continuous variables, which can be a
> little tricky. You cannot do it with the model that you have. The
> typical way to do this  is to create a third covariate which is the
> product of Performance*Age; you should remove the mean of Performance
> and Age before doing the product.
> >
> > Thanks.
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
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> 
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> 
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> 
>
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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
Outgoing: 

Re: [Freesurfer] FSGD and Contrast to determine the effect of age on performance

[Martin Juneja]

Thanks much Dough for your reply.

So if I add another column Performance*Age (after removing the mean of
each) in my fsgd file (and remove individual columns for Performance and
age), could you please tell what will be the contrast matrix (after only
Gender as a covariate) in that case i.e. for following fsgd:

Class Male
Class Female
Variables *Perform*Age*
Input S1 Male 180
Input S2 Female 167

Thanks.

On Mon, Feb 26, 2018 at 2:31 PM, Douglas N Greve 
wrote:

>
>
> On 02/24/2018 12:00 AM, Martin Juneja wrote:
> > Hi experts,
> >
> > I am not sure if this has already been addressed in FS discussion.
> >
> > If my fsgd file looks like following:
> >
> > Class Male
> > Class Female
> > Variables Performance Age
> > Input S1 Male 181 25
> > Input S2 Female 167 23
> > 
> > 
> >
> > I understand that the contrast matrix *[**0 0 1 -1 0 0]* represents
> > whether there is a difference between the group
> > (male/female)-performance slopesregressing out the effect of age. In
> > other words, this matrix calculates whether two slopes i.e. one for
> > males: thickness-performance slope and second for females:
> > thickness-performance slope - are significantly different after
> > regressing out the effect of age.
> >
> > My questions are following:
> >
> > (1) Is my above interpretation of contrast matrix*[**00 1 -1 0
> > 0]* correct?
> Yes
> > (2) If my interpretation is correct, then I was wondering what will be
> > the contrast matrix if *I want to check whether there is **significant
> > effect of age on e.g. thickness-performance slopes after regressing
> > out the effect of gender.* And what will be the corresponding fsgd
> > file for that, any changes in that?
> This is an interaction between continuous variables, which can be a
> little tricky. You cannot do it with the model that you have. The
> typical way to do this  is to create a third covariate which is the
> product of Performance*Age; you should remove the mean of Performance
> and Age before doing the product.
> >
> > Thanks.
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> 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
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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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
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> properly
> dispose of the e-mail.
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Re: [Freesurfer] FSGD and Contrast to determine the effect of age on performance

[Douglas N Greve]

On 02/24/2018 12:00 AM, Martin Juneja wrote:
> Hi experts,
>
> I am not sure if this has already been addressed in FS discussion.
>
> If my fsgd file looks like following:
>
> Class Male
> Class Female
> Variables Performance Age
> Input S1 Male 181 25
> Input S2 Female 167 23
> 
> 
>
> I understand that the contrast matrix *[**0 0 1 -1 0 0]* represents 
> whether there is a difference between the group 
> (male/female)-performance slopesregressing out the effect of age. In 
> other words, this matrix calculates whether two slopes i.e. one for 
> males: thickness-performance slope and second for females: 
> thickness-performance slope - are significantly different after 
> regressing out the effect of age.
>
> My questions are following:
>
> (1) Is my above interpretation of contrast matrix*[**00 1 -1 0 
> 0]* correct?
Yes
> (2) If my interpretation is correct, then I was wondering what will be 
> the contrast matrix if *I want to check whether there is **significant 
> effect of age on e.g. thickness-performance slopes after regressing 
> out the effect of gender.* And what will be the corresponding fsgd 
> file for that, any changes in that?
This is an interaction between continuous variables, which can be a 
little tricky. You cannot do it with the model that you have. The 
typical way to do this  is to create a third covariate which is the 
product of Performance*Age; you should remove the mean of Performance 
and Age before doing the product.
>
> Thanks.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
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] Creating ROI on the functional map

[Douglas N Greve]

I think it should work; We are not using tksurfer any more (freeview 
instead), but I think it should still work


On 02/23/2018 05:16 PM, Sarah Cole wrote:
> Hi,
>
> I was wondering if this method is still applicable in version 6 
> https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs
>
>
> I cannot seem to find any of the options for creating an ROI.
>
> Thank you,
>
> S
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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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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Re: [Freesurfer] Unknown Label in following postprocessing with mne-python

[Douglas N Greve]

I'm not sure I understand what you are asking about. Do you mean in the 
aseg.mgz or the aparc+aseg.mgz? Unknown is usually just stuff outside of 
the head, but sometimes can be in the head (eg, with aparc+aseg.mgz).


On 02/22/2018 08:51 AM, Daniel van de Velden wrote:
> Dear fellow colleagues,
>
>
> in my study I use volumetric source spaces. In the process of creating
> them, I decided to identify all available volumelabels FreeSurfer
> "recognized" in the given mri image.
>
> Every single subject inherits, despite all other volumelabels, a
> volumelabel called "Unknown". In an 3D representation of those "unknown"
> volumelabel coordinates I opine those points could also be part of other
> volumelabels like cerebral cortex or white matter.
>
> Would you please give me a detailed explanation of the origin of this
> 'Unknown' label? Specifically in respect to the fsaverage "subject".
>
>
> Best regards,
>
> Daniel van de Velden
>
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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
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Re: [Freesurfer] Extraction of cortical thickness in native space

[Douglas N Greve]

Can you be more specific about which step is failing and how you are 
verifying the failure?


On 02/21/2018 05:21 PM, Albrecht, Daniel S. wrote:
>
> Hello,
>
>
> We are attempting to extract cortical thickness values from a 
> pre-defined ROI in MNI space.
>
>
> Originally, we had followed the instructions detailed here:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
>
> for extraction in MNI space, but now wanted to extract thickness from 
> individual subject T1 images in native space.
>
>
> We attempted to use the same pipeline (e.g. register native space T1 
> to fsaverage) but were unable to get a good registration with several 
> different tools.
>
>
> Is there a better way to do this, either by improving the registration 
> to fsaverage, or by transforming the ROI to native space (which we 
> have done) and projecting that to a surface/label?
>
>
> Any suggestions are welcome, and we appreciate the help!
>
>
> Cheers,
>
>
> Dan
>
> VolumeRoiCorticalThickness - Free Surfer Wiki 
> 
> surfer.nmr.mgh.harvard.edu
> Cortical Thickness of a Volume-defined ROI. This page describes the 
> workflow to extract freesurfer cortical thickness values for a 
> region-of-interest (ROI) defined in ...
>
>
>
>
>
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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
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Re: [Freesurfer] local gyrification index - contrast and doss vs. dods

[Douglas N Greve]

On 02/21/2018 11:47 AM, C.P.E. Rollins wrote:
> Dear Freesurfer Developers,
>
> I'm following the very well-documented steps proposed by Marie Schaer
> for measuring local gyrification index in the paper "How to Measure
> Cortical Folding from MR Images: a Step-by-Step Tutorial to Compute
> Local Gyrification Index"
> (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/). I have 2
> questions I was wondering whether you might be able to answer:
>
> 1) Based on the contrast and FSDG files described in the paper (patients
> vs. controls, controlling for age and gender), would significant regions
> in blue refer to regions with reduced gyrification in patients relative
> to controls (patient LGI < control LGI) or vice versa?
Blue regions will be patient > control
>
> 2) When I try running the analysis in QDEC as opposed to command line
> with mri_glmfit, I get very different results - I think because QDEC is
> generating different contrast files than the one specified in the paper
> (1 1 -1 -1 0). Basically, this seems to be due to the difference in
> modelling LGI with doss (command line) or dods (default QDEC). I was
> wondering whether there were any reason doss was chosen for LGI instead
> of dods (see Step 5 in Section 4 Statistical Group Comparisons)?
It is not something related to LGI. It relates to how you think your 
data behave. See http://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss
>
> Thank you in advance for your help.
>
> Kindest regards,
> Colleen
>

-- 
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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Surface Errors

[Emily Schwartz]

Hi Doug,

They were initially reoriented for VBM analysis, but nothing else was changed 
(comparing original versus reoriented, there does not seem to be differences). 
The subjects are elderly (mean age = 74.08). We are investigating a new 
pre-dementia syndrome so there may be greater atrophy in some subjects, but the 
majority of the participants processed so far should be cognitively healthy.

MRI scanning was performed with a Philips 3T Achieva Quasar TX multinuclear 
MRI/MRS system equipped with a Dual Quasar High Performance Gradient System, 
32-channel broadband digital RF system, Quadrature T/R Head Coil, Rapid View 
reconstructor, Intera Achieva Scan-Tools Pro R2.5 Package, NetForum and 
ExamCards, and SENSE parallel imaging capability.

The T1-weighted whole head structural image was acquired using axial 3D-MP-RAGE 
parameters over a 240 mm FOV and 1.0 mm isotropic resolution, TE: 54.6 ms, TR: 
59.9 ms, with SENSE factor 2.5.
 
We really appreciate your help. Please let me know if you need any more info.

Best,

Emily

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 26, 2018 1:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Surface Errors

Hi Emily, I looked over these subjects. While a few of the flagged spots
are not really problems, most of them are true inaccuracies. I think the
underlying problem is that your data is pretty noisy and have some
ringing. What kind of acq was it? Scanner, field strength, pulse seq?
Was it acquired at 1mm resolution or was it resampled? It looks a little
blurry to me. What are the subject characteristics? I don't think there
is an easy way to fix it. This might not be fatal as the errors are
probably randomly distributed across space. If you have a good number of
subjects, then there might not be much of an effect on group maps.



On 02/22/2018 02:50 PM, Emily Schwartz wrote:
> Hi Doug,
>
> Attached are the point sets for the 3 subjects. For some issues, I put a 
> range of coordinate points. Let me know if you need anything else.
>
> Thanks!
>
> Emily
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, February 22, 2018 11:55 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Surface Errors
>
> got em. can you send me coordinates (col, row,slice) where you are
> seeing the errors? You can also create a point set in FreeView (under
> File->New PointSet)
>
>
> On 02/22/2018 08:48 AM, Emily Schwartz wrote:
>> Hi Doug,
>>
>> Great, thank you. I sent it to you via filedrop.
>>
>> Best,
>>
>> Emily
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Wednesday, February 21, 2018 4:52 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Surface Errors
>>
>> yes, filedrop should be find
>>
>> thanks
>>
>>
>> On 02/21/2018 04:44 PM, Emily Schwartz wrote:
>>> Hi Doug,
>>>
>>> I definitely can. I cannot use FTP from this computer for some reason. Can 
>>> I upload it via filedrop and should I send it to your email?
>>>
>>> Thanks,
>>>
>>> Emily
>>>
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Wednesday, February 21, 2018 4:29 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Surface Errors
>>>
>>> I'm a little surprised you are getting them so frequently. Can you
>>> upload a couple of subjects so I can take a look?
>>>
>>>
>>>
>>> On 02/21/2018 02:52 PM, Emily Schwartz wrote:
 Hi Doug,

 I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors 
 so often?

 Best,

 Emily
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, February 21, 2018 2:18 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Surface Errors

 btw, what verions of FS are you using?


 On 02/21/2018 01:25 PM, Emily Schwartz wrote:
> Got it, thank you so much!
>
> Best,
>
> Emily
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, February 21, 2018 10:23 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Surface Errors

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

[Bruce Fischl]

sorry Gabor, can you repost the rest of the thread? What was the artefact?

On Mon, 26 Feb 2018, Gabor Perlaki wrote:

> Does anybody else have a comment on the experienced artefact?
> 
>
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[Freesurfer] questions about the segamentation volume

[Ting Li]

Hi FreeSurfer Expert,

I followed the Anatomical ROI analysis tutorial and make a aseg.vol.table for 
the 40 subjects. However, the segment volume can various a lot in different 
subjects, such as Left-Lateral-Ventricle, Left-Inf-Lat-Vent. I attached a 
screenshot. Thanks for your response. 

Best wishes,
Ting

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Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

[Gabor Perlaki]

Does anybody else have a comment on the experienced artefact

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Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

[Gabor Perlaki]

Does anybody else have a comment on the experienced artefact?
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Re: [Freesurfer] Hippocampal Subfield Error

[Iglesias Gonzalez, Eugenio]

Dear Theo,
Can you please provide us with the command you executed, and the complete 
output logs?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of "AKUDJEDU, 
THEOPHILUS" 
Reply-To: Freesurfer support list 
Date: Monday, 26 February 2018 at 12:39
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal Subfield Error


Hi All,



I tried to run a subject through FreeSurfer 6.0 for hippocampal Subfield 
segmentation but exited with errors.



The content of the recon-all.error file is below.




SUBJECT CHRM2001
DATE Sun Feb 25 00:34:13 GMT 2018
USER 15233963
HOST psych-sl03
PROCESSOR x86_64
OS Linux
Linux psych-sl03 3.10.0-327.36.3.el7.x86_64 #1 SMP Mon Oct 24 16:09:20 UTC 2016 
x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
/opt/ohpc/pub/apps/freesurfer/6.0.0/bin/recon-all
PWD /home/15233963/freesurfer/SUBJECTS/CHRM2001/label
CMD mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a 
./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab CHRM2001 rh white






Will be glad if you can provide guidance.



Cheers



Theo



___

Theophilus Akudjedu

BSc, MSc, PhD Candidate

Room 202 Comerford Suite,

Clinical Science Institute,

Department of Psychiatry,

National University of Ireland, Galway



Phone: +353 838329602

Email: t.akudje...@nuigalway.ie

   rasni...@gmail.com



[mage removed by sender.]

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Re: [Freesurfer] Surface Errors

[Douglas N Greve]

Hi Emily, I looked over these subjects. While a few of the flagged spots 
are not really problems, most of them are true inaccuracies. I think the 
underlying problem is that your data is pretty noisy and have some 
ringing. What kind of acq was it? Scanner, field strength, pulse seq? 
Was it acquired at 1mm resolution or was it resampled? It looks a little 
blurry to me. What are the subject characteristics? I don't think there 
is an easy way to fix it. This might not be fatal as the errors are 
probably randomly distributed across space. If you have a good number of 
subjects, then there might not be much of an effect on group maps.



On 02/22/2018 02:50 PM, Emily Schwartz wrote:
> Hi Doug,
>
> Attached are the point sets for the 3 subjects. For some issues, I put a 
> range of coordinate points. Let me know if you need anything else.
>
> Thanks!
>
> Emily
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, February 22, 2018 11:55 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Surface Errors
>
> got em. can you send me coordinates (col, row,slice) where you are
> seeing the errors? You can also create a point set in FreeView (under
> File->New PointSet)
>
>
> On 02/22/2018 08:48 AM, Emily Schwartz wrote:
>> Hi Doug,
>>
>> Great, thank you. I sent it to you via filedrop.
>>
>> Best,
>>
>> Emily
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Wednesday, February 21, 2018 4:52 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Surface Errors
>>
>> yes, filedrop should be find
>>
>> thanks
>>
>>
>> On 02/21/2018 04:44 PM, Emily Schwartz wrote:
>>> Hi Doug,
>>>
>>> I definitely can. I cannot use FTP from this computer for some reason. Can 
>>> I upload it via filedrop and should I send it to your email?
>>>
>>> Thanks,
>>>
>>> Emily
>>>
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Wednesday, February 21, 2018 4:29 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Surface Errors
>>>
>>> I'm a little surprised you are getting them so frequently. Can you
>>> upload a couple of subjects so I can take a look?
>>>
>>>
>>>
>>> On 02/21/2018 02:52 PM, Emily Schwartz wrote:
 Hi Doug,

 I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors 
 so often?

 Best,

 Emily
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, February 21, 2018 2:18 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Surface Errors

 btw, what verions of FS are you using?


 On 02/21/2018 01:25 PM, Emily Schwartz wrote:
> Got it, thank you so much!
>
> Best,
>
> Emily
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, February 21, 2018 10:23 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Surface Errors
>
> Hi Emily
>
> it is a segmentation error, but it's a pretty small one. It will mess up
> the thickness in a region a few mm^2. You could fix it by editing the
> wm.mgz if you really care about that spot
>
> cheers
> Bruce
>
>
> On Wed, 21 Feb 2018, Emily Schwartz wrote:
>
>> Hi Doug,
>>
>> Thank you for getting back to me. I've attached two images (Slice165 and 
>> Slice166) with an arrow pointing to the location. I am new at this, so 
>> maybe I am wrong and it is not a segmentation error.
>>
>> I've also attached an additional image (Slice185) of what I think is a 
>> type of topological error that I often see multiple times in a subject. 
>> Is this a topological defect? If so, if it is only over 3 slices does it 
>> need to be corrected?
>>
>> Thanks again,
>>
>> Emily
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, February 20, 2018 4:59 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Surface Errors
>>
>> sorry, what kind of errors? I could not really tell from the images what
>> the 

[Freesurfer] aseg and aparcstats2table on longitudinal data

[Lisa Delalande]

Hi FreeSurfer experts,

I would like to use the asegstats2table and the aparcstats2table commands
on my longitudinal data, that have been processing following the
longitudinal pipeline (recon-all -cross, - base and finally -long). And I
have two questions :

1) Am I obliged to do the  long_stats_slopes --qdec
./qdec/longi_presentacio.qdec.table.dat --stats aseg.stats --meas volume
--do-avg --do-rate --do-pc1 --time months command before using the
aseg/aparc commands ?

2) And I would like to know which subjectsID I have to choose for the
command line, example :
asegstats2table --subjects *001_tp1 002_tp1*...etc. (cross)? OR *template_001
template_002*...etc (base)? OR *001_tp1.long.template_001
002_tp1.long.template_002*...etc (long)?
Knowing that it's for a comparison test-retest (microlongitudinal : 1
month).


Thanks you for your precious help,
Best regards,

Lisa
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Re: [Freesurfer] thickness measure in basal ganglia

[Bruce Fischl]

Hi Giovanni

do you mean a cerebellar parcellation? We have several prototypes but 
haven't distributed anything yet.


cheers
Bruce
On Mon, 26 Feb 2018, Giovanni de Marco 
wrote:



Hello,

is there an atlas for the cerebellum using freesurfer ?

Many thanks for the information.

Best
Giovanni

2018-01-11 9:15 GMT+01:00 de Marco :
  Many thanks Bruce for your rapid and clear response.
  Have a nice day
  Best
  Giovanni

  Envoyé de mon iPhone

  > Le 11 janv. 2018 à 02:27, Bruce Fischl  a 
écrit :
  >
  > Hi Giovanni​​
  >
  > the basal ganglia are little balls of gray matter, so I'm not sure how 
one would
  measure thickness there. We do supply volume for each nucleus
  >
  > cheers
  > Bruce
  >> On Thu, 11 Jan 2018, Giovanni de Marco wrote:
  >>
  >> Hello,​​
  >> ​​In stats-table,​​
  >> ​​I did'n​​
  >> t find the thickness of
  ​​>> ​​basal ganglia.
  ​​>> 
​​Please,
 c​​
  >> an we
  >> ​​get
  ​​>> ​​thickness
  ​​>> in
  ​​>> basal ganglia?
  >> (​​
  >> Ma​​
  >> ybe
  ​​>> ​​freesurfer measures​​
  >> only the cortical thickness)​​
  >> 
​​Many
 thanks for your response.​​
  >> 
​​Giovanni​​
  >> --
  >> Tel: +33 (0) 6 74 61 01 65
  >> demarco.giova...@gmail.com
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>
>
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at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
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> but does not contain patient information, please contact the sender and 
properly
> dispose of the e-mail.




--

Tel: +33 (0) 6 74 61 01 65
demarco.giova...@gmail.com

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Re: [Freesurfer] -make versus -all for edits

[Bruce Fischl]

Hi Arkadiy

-make all uses the makefile utility to only rerun the processing steps 
that are needed based on the timestamp of the various files in the 
subject's dir and a table of dependencies.


cheers
Bruce
On Mon, 26 Feb 2018, 
Maksimovskiy, Arkadiy wrote:




Dear Experts,

I was wondering if someone might be able to help me understand what the 
difference is between the
two commands below. It seems that they can be used interchangeably, because I 
can forsee a situation
in which one might not remember which command to run and also have done several 
types of
corrections. Or would the former (-make) method only work on with 1 edits?

Thanks,

Arkadiy

If you cannot remember which command to run, use the -make flag. Recon-all will 
automatically begin
at whichever point in the processing stream you made your edits.

recon-all -make all -subjid 

If you have corrected several types of errors, it is recommended that you 
re-run recon-all from the
beginning, to ensure that none of your edits were left out. (Running from 
autorecon1 will not save
you much time)

recon-all -all -subjid 

 

 

-- 

Arkadiy L. Maksimovskiy, Ph.D.

Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School


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[Freesurfer] -make versus -all for edits

[Maksimovskiy, Arkadiy]

Dear Experts,
I was wondering if someone might be able to help me understand what the 
difference is between the two commands below. It seems that they can be used 
interchangeably, because I can forsee a situation in which one might not 
remember which command to run and also have done several types of corrections. 
Or would the former (-make) method only work on with 1 edits?
Thanks,
Arkadiy
If you cannot remember which command to run, use the -make flag. Recon-all will 
automatically begin at whichever point in the processing stream you made your 
edits.
recon-all -make all -subjid 
If you have corrected several types of errors, it is recommended that you 
re-run recon-all from the beginning, to ensure that none of your edits were 
left out. (Running from autorecon1 will not save you much time)
recon-all -all -subjid 


--
Arkadiy L. Maksimovskiy, Ph.D.
Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School
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[Freesurfer] Hippocampal Subfield Error

[AKUDJEDU, THEOPHILUS]

Hi All,


I tried to run a subject through FreeSurfer 6.0 for hippocampal Subfield 
segmentation but exited with errors.


The content of the recon-all.error file is below.



SUBJECT CHRM2001
DATE Sun Feb 25 00:34:13 GMT 2018
USER 15233963
HOST psych-sl03
PROCESSOR x86_64
OS Linux
Linux psych-sl03 3.10.0-327.36.3.el7.x86_64 #1 SMP Mon Oct 24 16:09:20 UTC 2016 
x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
/opt/ohpc/pub/apps/freesurfer/6.0.0/bin/recon-all
PWD /home/15233963/freesurfer/SUBJECTS/CHRM2001/label
CMD mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a 
./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab CHRM2001 rh white




Will be glad if you can provide guidance.


Cheers


Theo


___

Theophilus Akudjedu

BSc, MSc, PhD Candidate

Room 202 Comerford Suite,

Clinical Science Institute,

Department of Psychiatry,

National University of Ireland, Galway


Phone: +353 838329602

Email: t.akudje...@nuigalway.ie

   rasni...@gmail.com



[https://ci6.googleusercontent.com/proxy/b9-AoNc-V0v85TZ_pj6puJTgX7uWBNlZdohjQM11hVJywIAEwXEGsHgEnDPLCI7oFsH_DknZswzkpzUMsK1_yk3OwzRkUZZ73VRhQq1-TF2aFt-1u2fB2jnkmTrpvirljLd9ciRy-A_D1eiTBaS6Xak0JKNMiKL1sBIdRVKUiqrLEkqWzllvsRAPy9j9Ed1nWXu4-QUpob0nkuM=s0-d-e1-ft#https://docs.google.com/uc?export=download=0Bw-d1Byh7ldEU2czeGlfMjNVOTg=0Bw-d1Byh7ldENkZtSlhueGFHdTFhVVFSa25xSmNvNGs4QXdNPQ]

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Re: [Freesurfer] thickness measure in basal ganglia

[Giovanni de Marco]

Hello,

is there an atlas for the cerebellum using freesurfer ?

Many thanks for the information.

Best
Giovanni

2018-01-11 9:15 GMT+01:00 de Marco :

> Many thanks Bruce for your rapid and clear response.
> Have a nice day
> Best
> Giovanni
>
> Envoyé de mon iPhone
>
> > Le 11 janv. 2018 à 02:27, Bruce Fischl  a
> écrit :
> >
> > Hi Giovanni​​
> >
> > the basal ganglia are little balls of gray matter, so I'm not sure how
> one would measure thickness there. We do supply volume for each nucleus
> >
> > cheers
> > Bruce
> >> On Thu, 11 Jan 2018, Giovanni de Marco wrote:
> >>
> >> Hello,​​
> >> ​​In stats-table,​​
> >> ​​I did'n​​
> >> t find the thickness of ​​
> >> ​​basal ganglia. ​​
> >> 
> ​​Please, c​​
> >> an we
> >> ​​get ​​
> >> ​​thickness ​​
> >> in ​​
> >> basal ganglia?
> >> (​​
> >> Ma​​
> >> ybe ​​
> >> ​​freesurfer measures​​
> >> only the cortical thickness)​​
> >> 
> 
> 
> 
> 
> ​​Many thanks for your response.​​
> >> 
> ​​Giovanni​​
> >> --
> >> Tel: +33 (0) 6 74 61 01 65
> >> demarco.giova...@gmail.com
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>



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Tel: +33 (0) 6 74 61 01 65
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