what is this in reference to?
Registered to the subject's anatomical volume (which registers to the surface for free anyways, if I understand correctly).
On Wed, Sep 6, 2017 at 1:38 AM, <freesurfer-request@nmr.mgh.harvard.edu> wrote:
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When replying, please edit your Subject line so it is more specific
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Today's Topics:
1. Re: controlling for Sex in a model using two continuous
variables onto CTh (Douglas N Greve)
2. Re: Multi-Subject Comparison in FreeSurfer (Douglas N Greve)
3. Re: group interaction with one continuous covariate and three
nuisance variables (two continuous, one dichotomous) (Douglas N Greve)
4. Re: Interpretting Brain Segmentation Volume to eTIV ratio
(Douglas N Greve)
5. Problem with ambiguous voxels? (Del Re, Elisabetta)
6. Re: patch for ribbon mgz failure (Douglas N Greve)
7. Re: upsampling ?h.curv (Douglas N Greve)
8. Re: Map of covariance (Douglas N Greve)
9. Fixed Effects Analysis on Single Subject's Brain
(Taylor, Johnmark)
10. Re: Freesurfer Preliminary Questions (Douglas N Greve)
11. Re: Occipital Cortex Segmentation (Douglas N Greve)
12. Re: How to estimate the Intracranial area? (Douglas N Greve)
13. Re: Combining Echo Frames Error (Douglas N Greve)
14. Re: individual mri_segstats waveforms for vertices or face in
label (Douglas N Greve)
15. Re: Fixed Effects Analysis on Single Subject's Brain
(Douglas N Greve)
16. Re: Reliability of labeling procedure in the same scan
(Mike Schmidt)
17. Re: Problem with ambiguous voxels? (Bruce Fischl)
18. Re: controlling for Sex in a model using two continuous
variables onto CTh (Uquillas, Federico D'Oleire)
19. MNI average brain in Freesurfer space (Anna Kasdan)
20. R: Re: Map of covariance (stdp82@virgilio.it)
21. Re: MNI average brain in Freesurfer space (Douglas N Greve)
22. Re: controlling for Sex in a model using two continuous
variables onto CTh (Douglas N Greve)
23. Re: R: Re: Map of covariance (Douglas N Greve)
24. Re: Cortical thickness (Douglas N Greve)
25. Re: sub-cortical analysis (Douglas N Greve)
26. Error with TRACULA using dcm and nii (Ferrier, Christopher Q.)
27. Re: controlling for Sex in a model using two continuous
variables onto CTh (Uquillas, Federico D'Oleire)
28. Re: controlling for Sex in a model using two continuous
variables onto CTh (Douglas N Greve)
29. Re: controlling for Sex in a model using two continuous
variables onto CTh (Uquillas, Federico D'Oleire)
30. Talairach registration error (Ariana Vajdi)
31. Ventricle Volumes Decreasing over time? (Tamara Tavares)
32. Re: Ventricle Volumes Decreasing over time? (Bruce Fischl)
33. Re: Talairach registration error (Douglas Greve)
34. ??: ROI (Jin Bo)
35. Re: wm topological defects (Ruotsalainen, Ilona)
------------------------------------------------------------ ----------
Message: 1
Date: Tue, 5 Sep 2017 12:01:32 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] controlling for Sex in a model using two
continuous variables onto CTh
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <c94e8853-6171-8520-1786-e46c2746e870@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=utf-8; format=flowed
can you send the fsgd file for the analysis that is failing?
On 08/29/2017 02:29 PM, Uquillas, Federico D'Oleire wrote:
> Dear FreeSurfer experts,
>
> We have run a vertex-wise analysis regressing a continuous variable
> onto cortical thickness on the surface, and would like to verify that
> our contrast that uses Age and Sex as covariates was defined
> correctly, especially since there is probably more than one way to
> control for a binary variable like Sex.
>
> On the website (https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss ) it
> suggests to make two regressors, one for Males, and one for Females,
> where for the former a 1 is indicative of the Male category, and a 1
> on the latter is indicative of the Female category. However, using
> that FSGD file and running a DOSS contrast as [0 1 0 0 0], we get the
> error: matrix is ill-condition or badly scaled, condno=2.01889e+07.
> We believe this may be due to the fact that Male and Female categories
> are autocorrelated and Freesurfer likes variables to be de-meaned.
> Running a FSGD file with only Age and our variable of interest via a
> DOSS contrast of [0 1 0] works without any errors.
>
> We thus created an FSGD file where we have Sex as our third variable
> (in addition to our continuous variable of interest and one demeaned
> continuous covariate), coding 1s for Males and 0s for Females, and we
> used a DOSS contrast of [0 1 0 0]. This provided us with a map that
> makes sense with our expectations.
>
> We would like to verify if this is doing what we believe it is doing;
> that is, looking at the relationship of our continuous variable or
> interest after accounting for age and sex.
> Any thoughts would be greatly appreciated.
>
> Thank you so much.
>
> Best,
>
> Fred
>
>
>
>
>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 2
Date: Tue, 5 Sep 2017 12:03:27 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Multi-Subject Comparison in FreeSurfer
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <36414cb1-e5cb-b192-d1a6-80259da31da4@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=windows-1252; format=flowed
You will need to run 500 different recon-all jobs. Obviously, if you run
them on a single computer, it will take a long time, so you will need
access to a cluster. Or you can buy time on a cloud service.
On 08/29/2017 02:54 PM, Sherrill, John T wrote:
>
> I am a new grad student and have been assigned a project in our Brain
> Imaging Research Center. I would be taking the time to push through
> and find these answers on my own but our program gives us 5 weeks of
> half days in a lab for a trial. So I am in a bit of a time crunch.
>
> I have been given a database of about 500 .nii files and been asked to
> find duplicates or likely duplicates. (Some subjects were
> duel-consented so they may have multiple scans.) What is the best way
> to recon-all all of the files? Individually, in small groups, or in
> one larger group? If I do it in groups do I need to list each file or
> can I just recon-all the entire directory? And if a recon-all on 1
> file takes 6-20hr, will doing a recon-all on the entire data set take
> 500*(6-20hr)=3000-10,000hr? Any help is greatly appreciated.
>
> John Sherrill
> jtsherrill@uams.edu
> john_sherrill@me.com
> (870) 761-0580
> ------------------------------------------------------------ ------------
> Confidentiality Notice: This e-mail message, including any
> attachments, is for the sole use of the intended recipient(s) and may
> contain confidential and privileged information. Any unauthorized
> review, use, disclosure or distribution is prohibited. If you are not
> the intended recipient, please contact the sender by reply e-mail and
> destroy all copies of the original message.
>
>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 3
Date: Tue, 5 Sep 2017 12:05:42 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] group interaction with one continuous
covariate and three nuisance variables (two continuous, one
dichotomous)
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <db68777a-81ed-d750-5075-cd6b35992588@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=utf-8; format=flowed
try looking at the FSGD examples for a case that you can generalize
https://surfer.nmr.mgh.harvard.edu/fswiki/ FsgdExamples
On 08/29/2017 08:59 PM, Ines M?rner-Lavanchy wrote:
>
> Dear FS experts,
>
> I would like to test if the correlations between thickness/area and
> cognition differ between two groups, while age, socioeconomic status
> (continuous) and gender (dichotomous) should be nuisance variables.
>
> To look at the effect of cognition in one group only, I made a model
> with 8 regressors:
>
> - sex male
> - sex female
> - age male
> - age female
> - cognition male
> - cognition female
> - ses male
> - ses female
>
> With the contrast 0 0 0 0 0.5 0.5 0 0: how does cognition correlate
> with Cth/CSA, controlled for age, sex, and ses.
>
> Now how do I model this, if I have *two* groups and want to look at
> the interaction of group*cognition? I have trouble setting up the fsgd
> and design matrix.
>
> Any help is appreciated,
>
> Thanks in advance,
>
> Ines
>
>
>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 4
Date: Tue, 5 Sep 2017 12:07:41 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Interpretting Brain Segmentation Volume to
eTIV ratio
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <3b478464-8cc5-e338-170a-0786a153e40a@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=windows-1252; format=flowed
I put that in there mainly as a quality check to automatically flag
something that has gone wrong. I think something went wrong if the value
is 0.65 (unless you have very atrophied subjects). You will have to take
a look to see what might have gone wrong.
On 08/29/2017 09:03 PM, Mehta, Chintan wrote:
>
> Dear FreeSurfer community,
>
>
> I wanted to interpret the BrainSegVol.to.eTIV ratio that is outputted
> from FreeSurfer version 5.2.0. In my sample of normally developing
> adolescents of ages 8 to 21, this ratio is between 0.65 and 0.85 for
> 98% of subjects. However, the value is less than 0.65 for 2% of subjects.
>
>
> Could this reflect actual feature of brain volume to eTIV?
>
>
> Or is this a reflection of poor scans, poor overall FreeSurfer
> processing, or inaccurate eTIV estimates for these subjects? Subjects
> with BrainSegVol.to.eTIV ratios less than 0.65 tended to all be
> females. They had Brain Segmentation volumes falling in normal ranges
> of females in the full sample. However, their eTIV was on the
> upper-end among eTIVs of females in the sample. If the eTIVs for these
> subjects were over-inflated, then it makes sense the ratios are
> especially low.
>
> Thank you.
>
> Best,
> Chintan
>
>
>
>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 5
Date: Tue, 5 Sep 2017 16:07:37 +0000
From: "Del Re, Elisabetta" <Elisabetta_DelRe@hms.harvard.edu >
Subject: [Freesurfer] Problem with ambiguous voxels?
To: "freesurfer@nmr.mgh.harvard.edu " <freesurfer@nmr.mgh.harvard.edu >
Cc: "Somes, Nathaniel G." <NSOMES@BWH.HARVARD.EDU>
Message-ID:
<CY4PR07MB2837476706EFA64ABABA2CAEB3960@CY4PR07MB2837. >namprd07.prod.outlook.com
Content-Type: text/plain; charset="iso-8859-1"
Dear FS Team,
We are running recon-all for a large dataset and 5 of the cases keep getting stuck at the exact same spot. It is the point at which the following has just been displayed on the screen:
#@# WM Segmentation Wed Aug 30 17:34:40 EDT 2017
mri_segment brain.mgz wm.seg.mgz
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (107.0): 105.5 +- 6.4 [91.0 --> 125.0]
GM (78.0) : 81.0 +- 6.1 [56.0 --> 94.0]
setting bottom of white matter range to 87.1
setting top of gray matter range to 93.2
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
For these 5 cases it will sit at this step apparently still running for over a week without any change before I cancel the job. There does not seem to be anything special about these 5 cases either in terms of their header information or visually. We have not found any artifacts in the images except for some minor ringing which is present in many images in the dataset, not just these. The rest of the cases of the dataset all ran to completion and produced all of the files we were expecting, but a subset of them seem to have a related issue where most of the wmparc.mgz labelmap is unsegmented white matter. Only the very edges and the very center are getting designated as something other than this label. The rest of the files in the "mri" directory such as aparc+aseg.mgz and so on are equally as affected by this. Do you know what could be going on here? I would be happy to give you any more information that could be helpful.
Best,
Elisabetta and Nate
Elisabetta C. del Re, Ph.D.
Assistant Professor of Psychiatry,
Department of Psychiatry
Harvard Medical School
phone 617 9675569
mail elisabetta_delre@hms.harvard.edu
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------------------------------
Message: 6
Date: Tue, 5 Sep 2017 12:09:31 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] patch for ribbon mgz failure
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <411ec6c7-19d3-3516-2972-ca668deae584@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=utf-8; format=flowed
Use the mri_segstats from this URL that is appropriate for your system
(eg, if you're running centos6, the download that patch and copy it to
mri_segstats)
https://surfer.nmr.mgh.harvard.edu/pub/dist/ freesurfer/5.3.0-patch/
On 08/30/2017 06:32 AM, Maria Gloria Rossetti wrote:
> Hi freesurfer team,
>
> I got the same error described here:
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard. edu/msg45983.html
> and, as suggested, I tried to copy in $FREESURFER_HOME/bin/ the patch
> from
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ greve/mri_segstats
> but I cannot find the URL.
> I also found some patches here :
> https://surfer.nmr.mgh.harvard.edu/pub/dist/ freesurfer/5.3.0-patch/
> but I don't know which one I'm supposed to use.
>
> Any advice?
>
> Thanks!
> Gloria
>
>
>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 7
Date: Tue, 5 Sep 2017 12:11:25 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] upsampling ?h.curv
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <b615e318-c277-9d08-f331-e55ab710d1cc@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=utf-8; format=flowed
You can also run
mris_apply_reg --src lh.curv --streg lh.white lh.white.upsampled --trg
lh.curv.upsampled.mgh
On 08/30/2017 01:17 PM, Bruce Fischl wrote:
> ?h.curv is just the spatially smoothed ?h.white.H. If you specify -a 10
> (average 10 times) it should be pretty close th ?h.curv
>
> On Wed, 30 Aug 2017,
> shahin@nmr.mgh.harvard.edu wrote:
>
>> Hi Bruce,
>> Would you be more specific. The command that you suggested generates
>> ?h.white.K and ?h.white.H. I am trying to generate ?h.curv.
>>
>>> try running
>>>
>>> mris_curvature -w <hires surface> ...
>>> On Wed, 30 Aug 2017,
>>> shahin@nmr.mgh.harvard.edu wrote:
>>>
>>>> Dear Freesurfers,
>>>> I want to project a map on up-sampled inflated brain. Up-sampled
>>>> inflated brain has been generated using mris_mesh_subdivide command
>>>> (without any problem). But when I apply the same command to ?h.cuv I
>>>> get an error message that:
>>>>
>>>> ERROR: MRISread: file 'surf/rh.curv' has many more faces than vertices!
>>>> Probably trying to use a scalar data file as a surface!
>>>>
>>>> I even tried to regenerate ?h.curv files using mris_make_surfaces as
>>>> below:
>>>>
>>>> mris_make_surfaces -c -white rh.white_upsampled subjid ?h
>>>>
>>>> But this command automatically down-sample rh.curv after
>>>> down-sampling
>>>> rh.white.
>>>>
>>>> Regards
>>>> _______________________________________________
>>>> 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
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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/
------------------------------
Message: 8
Date: Tue, 5 Sep 2017 12:12:54 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Map of covariance
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <0b274662-5761-884e-a39c-f59d1e1d7bbd@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=utf-8; format=flowed
I don't understand what you are asking. can you elaborate?
On 08/30/2017 12:50 PM, stdp82@virgilio.it wrote:
> Hi list,
> by applying a design e.g. 4GV1 in fsgd I could assess the dependence
> of group differences taking in account the effect of covariate.
> Anyway, where I should look if I want assess the the map showing the
> clusters in which the dependent variable is associated to covariate,
> tacking in account the group difference? Please could you suggest my
> the path?
> Thanks
>
> Stefano
>
>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 9
Date: Tue, 5 Sep 2017 12:15:33 -0400
From: "Taylor, Johnmark" <johnmarktaylor@g.harvard.edu>
Subject: [Freesurfer] Fixed Effects Analysis on Single Subject's Brain
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAOBxrqwbkRH4Y37PkL8O_bwoiQ7nRzbzcaLoeARjtuGidcrZJA@ >mail.gmail.com
Content-Type: text/plain; charset="utf-8"
Hello,
Quick question. If I scanned a single subject across several sessions and
want to do a fixed effects analysis on that subject's brain (without
registering to MNI or Talairach space), how do I go about doing this? I am
trying to us isxconcat-sess and then mri_glmfit, but I am not seeing an
option to simply do the analysis in native space instead of registering to
a standard brain. Is there a way to do this besides taking the end result
of the analysis and doing the reverse registration back to the subject's
brain?
JohnMark
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Message: 10
Date: Tue, 5 Sep 2017 12:15:57 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer Preliminary Questions
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <6a3ef912-75af-4aa0-bd40-69b20b3b7661@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=windows-1252; format=flowed
you have to create the directory before you can cd to it. If you don't
know how to create a directory in unix, then you should take some time
to learn unix before trying to run FS.
On 08/31/2017 12:22 PM, Ledesma, Jason wrote:
>
> Hi Bruce,
>
>
> Do you have any suggestions as to how to determine the correct
> directory and pathway to use?
>
>
> Sincerely,
>
> Jason Ledesma
> Staff Research Associate
> Phone: 1(424)571-7755
> E-mail: jason.ledesma@labiomed.org <mailto:jason.ledesma@labiomed.org >
>
> ------------------------------------------------------------ ------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of Ledesma, Jason
> <jason.ledesma@labiomed.org>
> *Sent:* Wednesday, August 30, 2017 1:39:30 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Freesurfer Preliminary Questions
>
> Bruce,
>
>
> It appears that the directory does not exist. See the following:
>
>
> fsuser@xubuntu-VirtualBox:~$ ls C:\tutorial data
> ls: cannot access C:tutorial: No such file or directory
> ls: cannot access data: No such file or directory
>
> fsuser@xubuntu-VirtualBox:~$ ls tutorial data
> ls: cannot access tutorial: No such file or directory
> ls: cannot access data: No such file or directory
>
> Here is what happens when doing a general ls command:
>
>
> fsuser@xubuntu-VirtualBox:~$ ls
> buckner_data-tutorial_subs error.log Pictures surfer.log Videos
> Desktop export Public tar
> Documents matlab setenv Templates
> Downloads Music source tutorial_data
> fsuser@xubuntu-VirtualBox:~$ ^C
> fsuser@xubuntu-VirtualBox:~$ ^C
> fsuser@xubuntu-VirtualBox:~$
>
>
> Sincerely,
>
> Jason Ledesma
> Staff Research Associate
> Phone: 1(424)571-7755
> E-mail: jason.ledesma@labiomed.org <mailto:jason.ledesma@labiomed.org >
>
> ------------------------------------------------------------ ------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of Bruce Fischl
> <fischl@nmr.mgh.harvard.edu>
> *Sent:* Wednesday, August 30, 2017 1:35:49 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Freesurfer Preliminary Questions
> thanks Jason
>
> does that directory exist? What happens if you try to ls it?
>
> Bruce
> On Wed, 30 Aug
> 2017, Ledesma, Jason wrote:
>
> >
> > Hi Bruce,
> >
> >
> > Here is the command that I tried and the resulting output/error message:
> >
> >
> > fsuser@xubuntu-VirtualBox:~$ export TUTORIAL_DATA=C:\tutorial data
> > fsuser@xubuntu-VirtualBox:~$ export
> SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs
> > fsuser@xubuntu-VirtualBox:~$ cd $SUBJECTS_DIR
> > bash: cd: C:tutorial/buckner_data/tutorial_subjs: No such file or
> directory
> > fsuser@xubuntu-VirtualBox:~$ ^C
> > fsuser@xubuntu-VirtualBox:~$
> >
> >
> > Sincerely,
> >
> > Jason Ledesma
> > Staff Research Associate
> > Phone: 1(424)571-7755
> > E-mail: jason.ledesma@labiomed.org
> >
> >
> ____________________________________________________________ ______________________________ __________
> > From: freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of
> > Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> > Sent: Wednesday, August 30, 2017 1:24:12 PM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] Freesurfer Preliminary Questions
> > Hi Jason
> >
> > in general it is much easier for us if you can cut and paste text into
> > the email. Pictures are useful for showing things in the data and such
> >
> > cheers
> > Bruce
> > On
> > Wed, 30 Aug 2017, Ledesma, Jason wrote:
> >
> > >
> > > Hi Bruce,
> > >
> > >
> > > Thank you for your quick response. Attached are photos in number
> order which should help to
> > explain my situation. The first three photos depict the tutorial data as
> > > they are downloaded into my computer. Photo 4 illustrates the
> version of Freesurfer that I am
> > using. Photos 5 and 6 express how the downloaded tutorial data
> folder has
> > > been shared to Freesurfer. Photo 7 illustrates an example of the
> commands I have used. I have
> > tried other pathways as well but am still unsure which the proper
> command
> > > should be. Unix is in fact new to me. Let me know if you require
> any other details. Looking
> > forward to hearing your thoughts.
> > >
> > >
> > > Sincerely,
> > >
> > > Jason Ledesma
> > > Staff Research Associate
> > > Phone: 1(424)571-7755
> > > E-mail: jason.ledesma@labiomed.org
> > >
> >
> >___________________________________________________________ ______________________________ __________
> > ____________________________________________________________ _________
> > > From: freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of
> > Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> > > Sent: Wednesday, August 30, 2017 12:10:24 PM
> > > To: Freesurfer support list
> > > Subject: Re: [Freesurfer] Freesurfer Preliminary Questions
> > > Hi Jason
> > >
> > > can you elaborate about what you mean by you "cannot interact with the
> > > data"?
> > >
> > > In general, please send us the full command you ran and all its screen
> > > output including whatever errros you encountered
> > >
> > > cheers
> > > Bruce
> > > On
> > > Wed, 30 Aug 2017, Ledesma, Jason wrote:
> > >
> > > >
> > > > To whom it may concern,
> > > >
> > > >
> > > > I am to attend the upcoming Freesurfer course session in Boston,
> and I would like to ask a few
> > preliminary questions. I am currently attempting to run Freesurfer 5.3
> > > > on a windows unit via the Oracle VM VirtualBox Manager. I have
> tried to follow the instructions
> > of the tutorial thus far, but am having trouble properly downloading
> > > the
> > > > tutorial data into Freesurfer (the data I am attempting to
> acquire can
> > be found at
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ ).OutputData_freeview
> I have
> > > > tried setting up a shared folder and placing the data in a
> "Machine Folder", but I still cannot
> > interact with the data. Do you know why this may be? I see that a
> > > > license key must first be obtained in some instances; perhaps
> this is the reason there are
> > issues. Also, what is the best way to download the most recent
> version of
> > > > Freesurfer on windows? Thank you.
> > > >
> > > >
> > > > Sincerely,
> > > >
> > > > Jason Ledesma
> > > > Staff Research Associate
> > > > Phone: 1(424)571-7755
> > > > E-mail: jason.ledesma@labiomed.org
> > > >
> >
> >>__________________________________________________________ ______________________________ __________
> > ____________________________________________________________ _________
> > > _
> > > > LA BioMed Warning: This email (and any attachments) is intended
> for the use of the person to
> > which it is addressed. It may contain information that is privileged and
> > > > confidential. As the recipient, you are obligated to maintain it
> in a safe, secure and
> > confidential manner. Unauthorized disclosure or failure to maintain
> > > > confidentiality may subject you to governmental penalties.
> Should you not be the intended
> > recipient, please notify us by return email, and delete this message
> from
> > > your
> > > > computer at once.
> > > >
> >
> >>__________________________________________________________ ______________________________ __________
> > ____________________________________________________________ _________
> > > _
> > > >
> > > >
> > >
> > >
> >
> >
>
>
> _______________________________________________
> 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
greve@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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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ greve/
------------------------------
Message: 11
Date: Tue, 5 Sep 2017 12:19:16 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Occipital Cortex Segmentation
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <93b6e482-3671-bbf5-071a-03c742f669c6@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=windows-1252; format=flowed
On 08/30/2017 03:57 PM, Torrado Carvajal, Angel wrote:
> Hello,
>
> I need to get the segmentation of the occipital cortex. I am
> attempting to generate the corresponding ROI, using the
> mri_annotation2label command and then running mris_anatomical_stats to
> merge the labels and get the actual volume. I am calling
> mri_annotation2label as follows:
>
> mri_annotation2label --subject <ID> --hemi lh --lobesStrict
> lobefile --outdir 'TEMP'
>
> However, I have a couple of questions:
>
> 1. Is there any way to generate both lh and rh together? Or should I
> generate separate volumes and then merge them?
>
For a surface-based segmentation, the hemispheres must be done separately
>
> 1.
>
>
> 2. What is the structure of the lobefile? I cannot find any example
> on the wiki.
>
This is the output annotation file (like lh.aparc.annot)
>
> 1.
>
> Thank you very much for your help!
> --
> *Angel Torrado-Carvajal*
> Postdoctoral Research Fellow
> Pain Neuroimaging Laboratory
> MGH/HST Athinoula A. Martinos Center for Biomedical Imaging
> Building 149, Room 1101, 13th Street, Charlestown, MA 02129 USA
> atorradocarvajal@mgh.harvard.edu | www.nmr.mgh.harvard.edu
> <http://www.nmr.mgh.harvard.edu > | @MGHMartinos
>
>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 12
Date: Tue, 5 Sep 2017 12:20:29 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to estimate the Intracranial area?
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <3e4d1dd1-a829-f333-8d76-23d0d861f537@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=UTF-8; format=flowed
do you mean the surface area of the inside of the skull? We do not
segment the skull, so no such area measure is possible.
On 08/30/2017 11:14 PM, Zhiliang Long wrote:
> Dear FS experts:
>
> I'am writting to ask for help about intracranial area. I can find
> the information of intracranial volume in aseg.stats file. But i did
> not find the information of intracranial area or is there any way to
> estimate the intracranial area ?
>
> Looking forward to any suggestions.
>
> best
> Zhiliang Long
>
>
>
>
>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 13
Date: Tue, 5 Sep 2017 12:21:58 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Combining Echo Frames Error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <eace550b-e6ef-0aa7-bbee-e7f4972a8b42@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=utf-8; format=flowed
the first question is whether this is multi-echo data? Assuming it is,
you can
mv 001.mgz multiecho.mgz
mri_concat --rms multiecho.mgz --o 001.mgz
On 08/31/2017 09:16 AM, Maksimovskiy, Arkadiy wrote:
>
> Dear Freesurfer experts,
>
> Here are the commands I entered, and errors I received:
>
> recon-all -subjid Test01 -i /Testing/T1_MEMPRAGE_4/IM-0002-0206.dcm
> -autorecon1
>
> #@# MotionCor Thu Aug 31 09:00:15 EDT 2017
>
> Found 1 runs
>
> /Users/amaksimovskiy/Desktop/Testing/Test01/mri/orig/001. mgz
>
> Checking for (invalid) multi-frame inputs...
>
> ERROR: input(s) cannot have multiple frames!
>
> /Users/amaksimovskiy/Desktop/Testing/Test01/mri/orig/001. mgz has 4 frames
>
> If this is a multi-frame MEMPRAGE image,
>
> use mri_concat --rms to combine echo frames.
>
> Could you please advice on how I can run the mri_concat --rms to
> combine echo frames? Also, would this have to be done before the
> autorecon1, and then reference the output (dicom or mgz?) into the
> recon-all command?
>
> Thank you for your help and information.
>
> - Arkadiy
>
> --
>
> Arkadiy L. Maksimovskiy, Ph.D.
>
> Postdoctoral Research Fellow
> McLean Imaging Center, McLean Hospital
> Department of Psychiatry, Harvard Medical School
>
>
>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 14
Date: Tue, 5 Sep 2017 12:24:59 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] individual mri_segstats waveforms for
vertices or face in label
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <1e1db9e4-3991-8345-035d-524263ac38a4@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=windows-1252; format=flowed
You could do it in matlab, something like
waveforms = fast_vol2mat(MRIread('waveform.nii.gz'));
% this will be a matrix ntimepoints by nvertices
You can then load the label with read_label.m and then pull out the
columns from waveforms that you want. Make sure to account for the fact
that the label indices are 0-based but matlab uses 1-based
On 08/31/2017 02:27 PM, Mcnorgan, Christopher wrote:
> Though one workaround might be to subdivide a label many, many times
> using mris_divide_parcellation, I was wondering if it is possible to
> obtain a per-vertex (or even per-face) fMRI waveform for a label. In
> other words, rather than compute the average waveform across all
> vertices, as with mri_segstats --label subject semi /path/to/label
> --avgwf avgwave.txt, which yields a single value that averages across,
> say, 5000 vertices, I would like to obtain each of the 5000 waveforms
> averaged over. I assume this would be more comparable to the scale of
> analysis used by those looking at voxel populations (e.g., as in MVPA).
>
> Thanks, Chris
>
> /**********************************************
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> * http://ccnlab.buffalo.edu/
> * Office: 716.645.0236
> * Lab: 716.645.0222
> **********************************************/
>
>
>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 15
Date: Tue, 5 Sep 2017 12:26:26 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Fixed Effects Analysis on Single Subject's
Brain
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <6767e602-90f5-496d-b5ae-fb608e509d01@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=utf-8; format=flowed
Do you mean in the native fMRI space or the native subject surface space?
On 09/05/2017 12:15 PM, Taylor, Johnmark wrote:
> Hello,
>
> Quick question. If I scanned a single subject across several sessions
> and want to do a fixed effects analysis on that subject's brain
> (without registering to MNI or Talairach space), how do I go about
> doing this? I am trying to us isxconcat-sess and then mri_glmfit, but
> I am not seeing an option to simply do the analysis in native space
> instead of registering to a standard brain. Is there a way to do this
> besides taking the end result of the analysis and doing the reverse
> registration back to the subject's brain?
>
> JohnMark
>
>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 16
Date: Tue, 5 Sep 2017 14:11:12 -0400
From: Mike Schmidt <mikeschmidt@schmidtgracen.com>
Subject: Re: [Freesurfer] Reliability of labeling procedure in the
same scan
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<CAAtzeZ5sMGnuaJdQUD6DY_t-USmeM2b5h5u28VMMt3LGx03LGg@ >mail.gmail.com
Content-Type: text/plain; charset="utf-8"
I've run many hundreds of scans repeatedly and found variance between
versions of FreeSurfer, but identical output within a version. Something
must have changed between runs. Perhaps you could try comparing the log
files and see where the deviations begin.
Mike Schmidt
On Sep 5, 2017 10:54 AM, "Phoolan Devi" <phoolandevi1989@gmail.com> wrote:
I mean the hippocampal volume in the aseg... so, it's not normal?
Bruce Fischl
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh. >harvard.edu&q=from:%22Bruce+ Fischl%22
Sat, 26 Aug 2017 11:24:44 -0700
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh. >harvard.edu&q=date:20170826
do you mean the hippocampal volume in the aseg or in the subfields?
On Sat, 26 Aug 2017, anonymous anonymous wrote:
Hi all,
Without noticing I run recon-all twice on the same scan of the same subject and
we noticed there are
some differences, at least in the hippocampal volume estimation.
Is it normal? If it is, why is it so?
Thank you so much for your help
This is a great community!
_______________________________________________
Freesurfer mailing
listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr. mgh.harvard.edu/mailman/ listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
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HelpLine athttp://www.partners.org/complianceline . If the e-mail was
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------------------------------
Message: 17
Date: Tue, 5 Sep 2017 14:14:55 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Problem with ambiguous voxels?
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Cc: "Somes, Nathaniel G." <NSOMES@BWH.HARVARD.EDU>
Message-ID:
<alpine.LRH.2.20.1709051414310.27393@gate.nmr. >mgh.harvard.edu
Content-Type: text/plain; charset="iso-8859-1"
really? I've never seen that. If you upload one of the subjects to our
ftp site (the entire subject dir tarred and gzipped) I will take a look
cheers
Bruce
On
Tue, 5 Sep 2017, Del Re, Elisabetta wrote:
>
> Dear FS Team,
>
> We are running recon-all for a large dataset and 5 of the cases keep getting stuck at the exact same spot. It is the point at which the following has
> just been displayed on the screen:
>
> #@# WM Segmentation Wed Aug 30 17:34:40 EDT 2017
>
> ?mri_segment brain.mgz wm.seg.mgz?
>
> doing initial intensity segmentation...
> using local statistics to label ambiguous voxels...
> computing class statistics for intensity windows...
> WM (107.0): 105.5 +- 6.4 [91.0 --> 125.0]
> GM (78.0) : 81.0 +- 6.1 [56.0 --> 94.0]
> setting bottom of white matter range to 87.1
> setting top of gray matter range to 93.2
> doing initial intensity segmentation...
> using local statistics to label ambiguous voxels...
>
>
>
> For these 5 cases it will sit at this step apparently still running for over a week without any change before I cancel the job. There does not seem to
> be anything special about these 5 cases either in terms of their header information or visually. We have not found any artifacts in the images except
> for some minor ringing which is present in many images in the dataset, not just these. The rest of the cases of the dataset all ran to completion and
> produced all of the files we were expecting, but a subset of them seem to have a related issue where most of the wmparc.mgz labelmap is unsegmented
> white matter. Only the very edges and the very center are getting designated as something other than this label. The rest of the files in the "mri"
> directory such as aparc+aseg.mgz and so on are equally as affected by this. Do you know what could be going on here? I would be happy to give you any
> more information that could be helpful.
>
> Best,
> Elisabetta and?Nate
>
>
>
> Elisabetta C. del Re, Ph.D.
> Assistant Professor of Psychiatry,
> Department of Psychiatry
> Harvard Medical School
> phone 617 9675569
> mail elisabetta_delre@hms.harvard.edu
>
>
>
>
>
------------------------------
Message: 18
Date: Tue, 5 Sep 2017 19:07:38 +0000
From: "Uquillas, Federico D'Oleire" <FUQUILLAS@mgh.harvard.edu>
Subject: Re: [Freesurfer] controlling for Sex in a model using two
continuous variables onto CTh
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<39EDC0F30613604782543DDC24F9B0130A70B16F@PHSX10MB13. >partners.org
Content-Type: text/plain; charset="us-ascii"
Dear Doug,
Sending the FSGD described in our original email as failing due to it being "ill-conditioned or badly scaled" with DOSS [0 1 0 0 0]. It is titled "FAILS_N47_edited_BL_CT_PiB_centAge_fsgd.txt".
The other one is the one that runs and gives expected results with a DOSS contrast [0 1 0 0].
Thanks so much.
Best regards,
Fred
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu ] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu]
Sent: Tuesday, September 05, 2017 12:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] controlling for Sex in a model using two continuous variables onto CTh
can you send the fsgd file for the analysis that is failing?
On 08/29/2017 02:29 PM, Uquillas, Federico D'Oleire wrote:
> Dear FreeSurfer experts,
>
> We have run a vertex-wise analysis regressing a continuous variable
> onto cortical thickness on the surface, and would like to verify that
> our contrast that uses Age and Sex as covariates was defined
> correctly, especially since there is probably more than one way to
> control for a binary variable like Sex.
>
> On the website (https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss ) it
> suggests to make two regressors, one for Males, and one for Females,
> where for the former a 1 is indicative of the Male category, and a 1
> on the latter is indicative of the Female category. However, using
> that FSGD file and running a DOSS contrast as [0 1 0 0 0], we get the
> error: matrix is ill-condition or badly scaled, condno=2.01889e+07.
> We believe this may be due to the fact that Male and Female categories
> are autocorrelated and Freesurfer likes variables to be de-meaned.
> Running a FSGD file with only Age and our variable of interest via a
> DOSS contrast of [0 1 0] works without any errors.
>
> We thus created an FSGD file where we have Sex as our third variable
> (in addition to our continuous variable of interest and one demeaned
> continuous covariate), coding 1s for Males and 0s for Females, and we
> used a DOSS contrast of [0 1 0 0]. This provided us with a map that
> makes sense with our expectations.
>
> We would like to verify if this is doing what we believe it is doing;
> that is, looking at the relationship of our continuous variable or
> interest after accounting for age and sex.
> Any thoughts would be greatly appreciated.
>
> Thank you so much.
>
> Best,
>
> Fred
>
>
>
>
>
> _______________________________________________
> 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
greve@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/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer
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------------------------------
Message: 19
Date: Tue, 5 Sep 2017 15:35:57 -0400
From: Anna Kasdan <anna.kasdan@nyu.edu>
Subject: [Freesurfer] MNI average brain in Freesurfer space
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAERmW5Zz__p7d9Z2c05v6DM6mBtVBt+ >Ase0jjX5cRvVE7jty5Q@mail. gmail.com
Content-Type: text/plain; charset="utf-8"
Hi everyone,
Is there a freesurfer file/file format for the *average* MNI brain (as
opposed to fsaverage which is just based on different subjects)? Or is
there a way to turn MNI coordinates into freesurfer space? Thanks so much!
Anna
Research Assistant, NYU
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------------------------------
Message: 20
Date: Tue, 5 Sep 2017 22:32:30 +0200 (CEST)
From: <stdp82@virgilio.it>
Subject: [Freesurfer] R: Re: Map of covariance
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<1024798845.2281131504643550527.JavaMail. httpd@fep-webmail-11.iol.local >
Content-Type: text/plain;charset="UTF-8"
Hi,
e.g., by considering two or more groups, I would like to map the clusters
reporting the covariance between the functional connectivity or cortical
thickness (dependent variable) and age, tacking in account the group
differences.
Instead, I'm not interested to map the group differences, taking in account
the nuisance factors.
Thanks,
Stefano
>----Messaggio originale----
>Da: "Douglas N Greve" <greve@nmr.mgh.harvard.edu>
>Data: 5-set-2017 18.12
>A: <freesurfer@nmr.mgh.harvard.edu >
>Ogg: Re: [Freesurfer] Map of covariance
>
>I don't understand what you are asking. can you elaborate?
>
>
>On 08/30/2017 12:50 PM, stdp82@virgilio.it wrote:
>> Hi list,
>> by applying a design e.g. 4GV1 in fsgd I could assess the dependence
>> of group differences taking in account the effect of covariate.
>> Anyway, where I should look if I want assess the the map showing the
>> clusters in which the dependent variable is associated to covariate,
>> tacking in account the group difference? Please could you suggest my
>> the path?
>> Thanks
>>
>> Stefano
>>
>>
>> _______________________________________________
>> 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
>greve@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/
>
>_______________________________________________
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer
>
>
>The information in this e-mail is intended only for the person to whom it is
>addressed. If you believe this e-mail was sent to you in error and the e-mail
>contains patient information, please contact the 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.
>
>
------------------------------
Message: 21
Date: Tue, 5 Sep 2017 16:45:26 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MNI average brain in Freesurfer space
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <014d3521-77dc-c66a-bf07-fa57b0f19bc9@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=utf-8; format=flowed
not sure what you mean, but check out the use cases here
https://surfer.nmr.mgh.harvard.edu/fswiki/ CoordinateSystems
On 09/05/2017 03:35 PM, Anna Kasdan wrote:
> Hi everyone,
>
> Is there a freesurfer file/file format for the /average/ MNI brain (as
> opposed to fsaverage which is just based on different subjects)? Or is
> there a way to turn MNI coordinates into freesurfer space? Thanks so much!
>
> Anna
> Research Assistant, NYU
>
>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 22
Date: Tue, 5 Sep 2017 16:57:05 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] controlling for Sex in a model using two
continuous variables onto CTh
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <730b79fd-0c5a-9529-ea4c-71b457a70e3f@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=windows-1252; format=flowed
in the one that fails you are including the binary gender as a
continuous variable, which will fail in FSGD. All catagorical variables
need to be coded as classes. see
https://surfer.nmr.mgh.harvard.edu/fswiki/ FsgdExamples
On 09/05/2017 03:07 PM, Uquillas, Federico D'Oleire wrote:
> Dear Doug,
>
> Sending the FSGD described in our original email as failing due to it being "ill-conditioned or badly scaled" with DOSS [0 1 0 0 0]. It is titled "FAILS_N47_edited_BL_CT_PiB_centAge_fsgd.txt".
>
> The other one is the one that runs and gives expected results with a DOSS contrast [0 1 0 0].
>
> Thanks so much.
>
> Best regards,
>
> Fred
>
> ________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu ] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu]
> Sent: Tuesday, September 05, 2017 12:01 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] controlling for Sex in a model using two continuous variables onto CTh
>
> can you send the fsgd file for the analysis that is failing?
>
>
> On 08/29/2017 02:29 PM, Uquillas, Federico D'Oleire wrote:
>> Dear FreeSurfer experts,
>>
>> We have run a vertex-wise analysis regressing a continuous variable
>> onto cortical thickness on the surface, and would like to verify that
>> our contrast that uses Age and Sex as covariates was defined
>> correctly, especially since there is probably more than one way to
>> control for a binary variable like Sex.
>>
>> On the website (https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss ) it
>> suggests to make two regressors, one for Males, and one for Females,
>> where for the former a 1 is indicative of the Male category, and a 1
>> on the latter is indicative of the Female category. However, using
>> that FSGD file and running a DOSS contrast as [0 1 0 0 0], we get the
>> error: matrix is ill-condition or badly scaled, condno=2.01889e+07.
>> We believe this may be due to the fact that Male and Female categories
>> are autocorrelated and Freesurfer likes variables to be de-meaned.
>> Running a FSGD file with only Age and our variable of interest via a
>> DOSS contrast of [0 1 0] works without any errors.
>>
>> We thus created an FSGD file where we have Sex as our third variable
>> (in addition to our continuous variable of interest and one demeaned
>> continuous covariate), coding 1s for Males and 0s for Females, and we
>> used a DOSS contrast of [0 1 0 0]. This provided us with a map that
>> makes sense with our expectations.
>>
>> We would like to verify if this is doing what we believe it is doing;
>> that is, looking at the relationship of our continuous variable or
>> interest after accounting for age and sex.
>> Any thoughts would be greatly appreciated.
>>
>> Thank you so much.
>>
>> Best,
>>
>> Fred
>>
>>
>>
>>
>>
>> _______________________________________________
>> 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
> greve@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/
>
> _______________________________________________
> 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
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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/
------------------------------
Message: 23
Date: Tue, 5 Sep 2017 16:59:44 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] R: Re: Map of covariance
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <c0db46ca-5260-c4c1-fe07-08f9ad091cd5@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=utf-8; format=flowed
you would need to create a contrast to look for the interaction. If you
have four gruops and 1 covariate, then it would be
0 0 0 0 1 -1 0 0
0 0 0 0 1 0 -1 0
0 0 0 0 1 0 0 -1
On 09/05/2017 04:32 PM, stdp82@virgilio.it wrote:
> Hi,
> e.g., by considering two or more groups, I would like to map the clusters
> reporting the covariance between the functional connectivity or cortical
> thickness (dependent variable) and age, tacking in account the group
> differences.
> Instead, I'm not interested to map the group differences, taking in account
> the nuisance factors.
> Thanks,
> Stefano
>
>> ----Messaggio originale----
>> Da: "Douglas N Greve" <greve@nmr.mgh.harvard.edu>
>> Data: 5-set-2017 18.12
>> A: <freesurfer@nmr.mgh.harvard.edu >
>> Ogg: Re: [Freesurfer] Map of covariance
>>
>> I don't understand what you are asking. can you elaborate?
>>
>>
>> On 08/30/2017 12:50 PM, stdp82@virgilio.it wrote:
>>> Hi list,
>>> by applying a design e.g. 4GV1 in fsgd I could assess the dependence
>>> of group differences taking in account the effect of covariate.
>>> Anyway, where I should look if I want assess the the map showing the
>>> clusters in which the dependent variable is associated to covariate,
>>> tacking in account the group difference? Please could you suggest my
>>> the path?
>>> Thanks
>>>
>>> Stefano
>>>
>>>
>>> _______________________________________________
>>> 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
>> greve@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/
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the 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.
>>
>>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 24
Date: Tue, 5 Sep 2017 17:07:00 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Cortical thickness
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <20c1b9e1-1e05-92b8-218d-50ea38855f4b@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=windows-1252; format=flowed
You need to map them into the same space. You can use mris_apply_reg to
map one subject into the other or you can use mris_preproc to put them
both into fsaverage space
On 09/01/2017 10:29 AM, Esteban, Eva(GE Healthcare) wrote:
>
> Hello everyone,
>
> I am trying to compare the difference in cortical thickness between
> two subjects by overlaying the surfaces (lh.thickness and r
> rh.thickness) but -diff doesn?t seem to be doing the work. Does anyone
> know of any other commands which could be useful for this?
>
> Thank you!
>
> Eva
>
>
>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 25
Date: Tue, 5 Sep 2017 17:41:37 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] sub-cortical analysis
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <d57c2714-2dc2-dd8d-3c02-92f705e57f75@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset=utf-8; format=flowed
I've added a voxel-based analysis to the wiki page
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
Note that I'm recommending using permutation instead of GRF for
correction of multiple comparisons
On 08/29/2017 10:03 AM, John Anderson wrote:
>
> Hi Dr Greve,
>
> I am using pet surfer to analyze suv images. I followed all the steps
> in wiki, I used the option mgx then I fed the
> imagesmgx.{ctxgm,subctxgm,gm} into surface based analysis for left and
> right hemispheres. I want to inquire about the sub cortical analysis.
>
> 1. I assume the analysis for sub cortical gray matter (i.e. using the
> imagessubctxgm) is volumetric. Is this correct?
>
Yes. This is on the wiki page.
>
> 2. Are the following steps correct for sub cortical gray matter analysis
>
> mri_vol2vol --movsubctxgm.nii.gz --reg reg.dat --tal --talres 2
> --talxfm talairach.xfm --nearest --no-save-reg --osubctxgm.tal2mm.nii.gz
>
> mri_masksubctxgm.tal2mm.nii.gz
> $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort. mask.mgzsubctxgm.tal2mm_subc. nii.gz
> &
>
> Concatenate all subjects together using mri_concat
>
> smooth using mri_fwhm (what is the recommended smoothing for suv)?
>
> Then Group analysis:
>
> mri_glmfit --y all.suvr.tal2mm.subc.sm10.nii --fsgd fsgd.dat --C
> contrast.mtx --glmdir dir
>
> mri_glmfit-sim --glmdir dir --grf 1.3 pos --cwpvalthresh 0.0166
>
> for "mri_glmfit-sim" in subcortical structure is the flag grf
> correct or cache?
>
>
> Thanks in advance!
> John
>
>
>
>
>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 26
Date: Tue, 5 Sep 2017 21:50:33 +0000
From: "Ferrier, Christopher Q." <cferri@lsuhsc.edu>
Subject: [Freesurfer] Error with TRACULA using dcm and nii
To: "freesurfer@nmr.mgh.harvard.edu " <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<D2E5A316DD989C45A1C50853D8EE4B7424B6AA97@SH-ExchMB1.master. >lsuhsc.edu
Content-Type: text/plain; charset="iso-8859-1"
Hi Freesurfer Team!. We are trying to use TRACULA to analyze the structural connectivity of PD patients scanned on a 3 tesla Philips Ingenia. We have run the tutorial data without any problems but encounter errors when using our own data. We ran recon-all on all of our subjects without any problem and follow the exact steps that worked for the tutorial data but encounter different errors when using the dcm or nii version of the DTI scans. Our nii files go from scanner to CD to Osirix to DICOM to dcm2nii which gives us the nii files and the bvals and bvecs. Here is the error for the nii DTI scans (included bvals and gradients in the config file for the nii files).
[Christinas-iMac:Freesurfer_temp/PD800/diffusion_recons] christina% trac-all -prep -c/Volumes/CFERRIER/ Freesurfer_temp/PD800/dmrirc. tutorial
ERROR: flag -c/Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc. tutorial unrecognized
-prep -c/Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc. tutorial
[Christinas-iMac:Freesurfer_temp/PD800/diffusion_recons] christina% trac-all -prep -c /Volumes/CFERRIER/Freesurfer_ temp/PD800/dmrirc.tutorial
INFO: SUBJECTS_DIR is /Volumes/CFERRIER/Freesurfer_temp/PD800/diffusion_recons
INFO: Diffusion root is /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT
Actual FREESURFER_HOME /Applications/Freesurfer
trac-preproc -c /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ scripts/dmrirc.local -log /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ scripts/trac-all.log -cmd /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ scripts/trac-all.cmd
#-------------------------------------
/Applications/Freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Thu Aug 31 14:45:46 CDT 2017
mri_convert --bvec-voxel /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI_ combined.nii /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI_ combined.nii /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI_ combined.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999339, -0.0363145, -0.00163044)
j_ras = (-0.0363101, 0.99508, 0.0921851)
k_ras = (0.00172524, -0.0921834, 0.995741)
writing to /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig.nii.gz...
cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvecs/PD800_bvecs. txt /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig.bvecs
cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvals/PD800_bvals. txt /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig.bvals
mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/bvecs.tmp /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig.bvecs
mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/bvals.tmp /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig.bvals
orientLAS /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig.nii.gz /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -9.1875
mri_convert -oni 128 -onj 128 -onk 50 -oid -0.999339 -0.0363145 -0.00163044 -ojd -0.0363101 0.99508 0.0921851 -okd 0.00172524 -0.0921834 0.995741 -oc 7.38609 19.7949 1.17333 -rt nearest /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig.nii.gz /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 128 -onj 128 -onk 50 -oid -0.999339 -0.0363145 -0.00163044 -ojd -0.0363101 0.99508 0.0921851 -okd 0.00172524 -0.0921834 0.995741 -oc 7.38609 19.7949 1.17333 -rt nearest /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig.nii.gz /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig_las.nii.gz
normalizing out_i_direction: (-0.999339, -0.0363145, -0.00163044) -> (-0.999339, -0.0363145, -0.00163044)
normalizing out_j_direction: (-0.0363101, 0.99508, 0.0921851) -> (-0.0363101, 0.99508, 0.0921851)
normalizing out_k_direction: (0.00172524, -0.0921834, 0.995741) -> (0.00172524, -0.0921834, 0.995741)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999339, -0.0363145, -0.00163044)
j_ras = (-0.0363101, 0.99508, 0.0921851)
k_ras = (0.00172524, -0.0921834, 0.995741)
Reslicing using nearest
writing to /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig_las.nii.gz...
INFO: found /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig.bvals, copying
INFO: found /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig.bvecs, converting to LAS
mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig_las.bvecs /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/bvecs
mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig_las.bvals /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/bvals
eddy_correct /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_orig_las.nii.gz /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi.nii.gz 0
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0000
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0001
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0002
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0003
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0004
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0005
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0006
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0007
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0008
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0009
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0010
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0011
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0012
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0013
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0014
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0015
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0016
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0017
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0018
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0019
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0020
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0021
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0022
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0023
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0024
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0025
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0026
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0027
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0028
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0029
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0030
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0031
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0032
processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi_tmp0033
mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/bvecs /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/bvecs.norot
xfmrot /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi.ecclog /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/bvecs.norot /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/bvecs
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
ln -sf /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi.nii.gz /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/data.nii.gz
mri_convert --frame 34 /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi.nii.gz /Volumes/CFERRIER/Freesurfer_ temp/PD800/TRAC_OUTPUT/PD800/ dmri/lowb.nii.gz
mri_convert.bin --frame 34 /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/ dmri/dwi.nii.gz /Volumes/CFERRIER/Freesurfer_