Re: [Freesurfer] Repost: Converting BV ROIs to FS

[Bruce Fischl]

Hi Katie

you can view data on a  tal brain by mapping the data using the 
talairach.xfm transform. Since you can also use the inverse of the 
transform you can map both ways. I think there is a tcl command in tksurfer 
for finding the vertex that is closest to a given tal coord. Try:


select_talairach_point   

cheers
Bruce


On Tue, 4 Sep 2012, Katie Bettencourt wrote:


Hrm.  Ok, is there any way to view data for a subject in Freesurfer on a
talairach transformed brain? What I would be hoping to do is bring up the
data in native subject space, make any ROI label, then also bring the data
up on a talairach transformed brain, make a ROI label, then put both labels
on the same brain (either native or talairach transformed) and see if they
are any different.
Also, is there a way to input a particular talairach vertex and jump to that
in freesurfer, instead of just moving the mouse around and hoping to find
the right spot?

Katie

On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl 
wrote:
  Hi Katie

  I don't think anyone here knows how to do this as we don't use
  it. Perhaps the Brain Voyager people do?

  sorry,
  Bruce
  On Tue, 4 Sep 2012, Katie Bettencourt wrote:


      So our lab is running a couple analyses and we
are getting different results based on whether we
use Brain Voyager or
      Freesurfer that we think is due to different
ROI selection across the two platforms.  Is there
anyway to load a
      BrainVoyager ROI into freesurfer?  The BV data
has been talairach transformed, does that matter?
 Less optimal would
      be loading a freesurfer ROI into BV, but if
that's easier, we could try that way too.
Any help would be appreciated.

Katie






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Re: [Freesurfer] repeated measures ANOVA with two groups

[Douglas N Greve]

Hi Shannon, sorry for the delay. There are several ways you can do this. 
If you already have a slope for each subject, then just use that as 
input and use the simple two group FSGD file. If you really want to do 
the RM ANOVA, then there are two ways. The simpler way is to create a 
"stack" of all subjects for each visit (eg, v1, v2, and v3) using 
mris_preproc. Next compute paired differences d12 = v1-v2 and d13 = 
v1-v3 using fscalc (note that you do not need v2-v3). Next, create a new 
stack from d12 and d13 with mri_concat (eg, mri_concat d12.mgh d13.mgh 
--o d12+d13.mgh). Then create an FSGD file with a class for each group 
and two variables (d12 and d13)). The structure will look something like 
this:

Input subject1 G1 1 0
Input subject2 G1 1 0
... rest of subjects for group 1 ...
Input subject1 G1 0 1
Input subject2 G1 0 1
... rest of subjects for group 1 ...
Input subject1 G2 1 0
Input subject2 G2 1 0
... rest of subjects for group 2 ...
Input subject1 G2 0 1
Input subject2 G2 0 1
... rest of subjects for group 2 ...

Run the analysis with DOSS. You can use the following contrast matrix to 
test for an interaction:
[1 -1 -1 1]

Let me know if that makes sense or not
doug



On 08/23/2012 09:39 PM, Shannon Kogachi wrote:
> Hi,
>   Is there a way to set up a repeated measures ANOVA and ANCOVA with 
> two different groups (ex: study group v. controls) and each subject 
> has more than two timepoints? Would it be possible to assign each 
> Input in the fsgd file to two classes (ex: timepoint scan and group) 
> or is there another way to set up the fsgd file and contrast matrices? 
> I've already used qdec in freesurfer 5.1 to calculate rates of change 
> and symmetrized percent changes between the timepoints (using 
> long_mris_slopes) but now would like to perform a repeated measures 
> test. Thank you!
>
> -Shannon K.
>
>
> ___
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] freesurfer tutorial data

[Help Desk -- Paul Raines]

Instead of FTP, you could try getting the files via HTTP at

http://surfer.nmr.mgh.harvard.edu/ftp/dist/freesurfer/

-- Paul Raines (http://help.nmr.mgh.harvard.edu)



On Tue, 4 Sep 2012 6:19pm, Dix Meiberth wrote:


Thx for your responses. But no, I try to copy to my harddrive on my 1 year old 
Mac. I think for the fith time right now. There should be no limit but I will 
doublecheck.

Best regards.

Dix

Von meinem iPhone gesendet

Am 04.09.2012 um 20:56 schrieb Help Desk -- Paul Raines 
:


2GB sounds like you reaching maybe a file size limit of your operating
system if it is really old. Or if you have are trying to download to a
FAT formated external USB drive or such.

-- Paul Raines (http://help.nmr.mgh.harvard.edu)



On Mon, 3 Sep 2012 11:32am, Bruce Fischl wrote:


Hi Dix,

not sure what's going on. Have you tried multiple times?

Bruce

On Mon, 3 Sep 2012, dix.meibe...@ukb.uni-bonn.de wrote:


Dear sirs and madames,
unfortunately I wasn't able to download the tutorial data for freesurfer.
The download interrupted at 2 GB within the
"bruckner_data_tutorial_subjs.tar.gz"
I already did the recon_all process for 90 brains and wanted to improve my
skills for the corrections.
Is there any advise you can give to get the tutorial data?
Best regards,
Dix Meiberth
(B.Sc. Neurowissenschaften)
Funktionelle Bildgebung
Klinik und Poliklinik für Psychiatrie und Psychotherapie
Universitätsklinikum Bonn
Sigmund-Freud-Strasse 25
53105 Bonn
Tel. 0228-287-16366
dix.meibe...@ukb.uni-bonn.de





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Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri

[Douglas N Greve]

Hi Longchuan, when I asked for the terminal output, I meant the stuff 
that gets printed to the screen when the command runs. Try running it 
outside of your script to capture the output. Also, does the old program 
require 20G ?
doug

On 08/27/2012 04:20 PM, Longchuan Li wrote:
> Hi, Doug
> Here is the output from my log file and my command. I have been 
> running this command many times and sometimes the job got killed, but 
> sometimes they finished without error.
>
> /usr/local/sge/bitc/spool/node13/job_scripts/77912: line 7: 30345 
> Killed  
> /home/lli/freesurferv51/bin/mri_label2vol.linux --offset 1 --annot 
> /home/lli/freesurferv51/subjects/RVJ8_Preuss_2015/label/rh.randomroi300_WithoutMedialWall.MacaqueYerkes6_to_RVJ8_Preuss_2015.annot
>  
> --temp 
> /home/lli/freesurferv51/subjects/RVJ8_Preuss_2015/mri/brain.mgz 
> --subject RVJ8_Preuss_2015 --hemi rh --fillthresh 0 --proj frac 0 
> 0.5 0.05 --o 
> /home/lli/freesurferv51/subjects/RVJ8_Preuss_2015/mri/rh.randomroi300_WithoutMedialWall_Ribbon.MacaqueYerkes6_to_RVJ8_Preuss_2015_fill0_projs0_proje0.5_projin0.05.nii.gz
>  
> --identity
>
> Many thanks in advance!
>
> Longchuan
>
>
> 
> *From:* Douglas Greve 
> *To:* Longchuan Li 
> *Cc:* FreeSurfer 
> *Sent:* Monday, August 27, 2012 3:47 PM
> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to 
> transfer ic2.tri
>
> What is your command line and what is the terminal output?
> doug
>
>
> On 8/27/12 7:57 PM, Longchuan Li wrote:
>> Hi, Doug
>>
>> This is a follow-up question regarding an updated code you sent to me 
>> earlier (mri_label2vol.linux). I noticed that this program frequently 
>> takes around ~20G RAM to run and easily get killed by Linux (I 
>> supposed) when I ran multiple subjects, because of the large amount 
>> of RAM used. Has anyone else proposed the issue? and if so, do you 
>> have any suggestions on solving the issue?
>>
>> Thank you!
>>
>> Longchuan
>>
>> 
>> *From:* Leon  
>> *To:* Douglas N Greve  
>> 
>> *Cc:* FreeSurfer  
>> 
>> *Sent:* Friday, June 8, 2012 3:48 PM
>> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to 
>> transfer ic2.tri
>>
>> Hi, Doug
>> I have run and checked the data and the problem has been perfectly 
>> solved. Thank you for the help!
>>
>> Leon
>>
>> 
>> *From:* Douglas N Greve  
>> 
>> *To:* Leon  
>> *Cc:* FreeSurfer  
>> 
>> *Sent:* Friday, June 8, 2012 1:32 PM
>> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to 
>> transfer ic2.tri
>>
>> I've put a new version of mri_label2vol at that ftp site. When you run
>> it, add "--offset 1". This will change the segmentations IDs to go from
>> 1-162 instead of 0-161.
>> doug
>>
>> On 06/08/2012 11:30 AM, Leon wrote:
>> > Hi, Douglas
>> >
>> > I checked the data this morning and confirmed that the missing ROI in
>> > the volume space is vertex_0 (see attached). Totally there are 162
>> > entries in the annotation file, but only 161 left in the volume file
>> > after transferring the annotation file to the volume using
>> > mri_label2vol and the intensity value ranges from 1 to 161.
>> >
>> > Thanks
>> >
>> > Leon
>> >
>> > PS: I am sending the message again because I was told that the image
>> > for the previous mail is too big.
>> >
>> > *From:* Leon mailto:leonad...@yahoo.com>>
>> > *To:* Douglas N Greve > >
>> > *Cc:* FreeSurfer > >
>> > *Sent:* Thursday, June 7, 2012 10:52 PM
>> > *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to
>> > transfer ic2.tri
>> >
>> > Hi, Douglas
>> >
>> > Thank you very much for taking care of it. The ROIs ending with 2 and
>> > 5s have been correctly labeled and have volumes now after running the
>> > fixed version of mris_make_face_parcellation.  However, there is still
>> > one ROI missing in the volume data that is located at the top of the
>> > postcentral gyrus after the annotation file was transferred from the
>> > subject's surface to the volume using mri_label2vol. I checked the
>> > index of the ROI yesterday (I am at home now and do not have access to
>> > the data) and I remember the index of the missing ROI is  vertex_0 and
>> > the location of the ROI is identical as the one in the picture I
>> > attached in the previous email. Do you think it might be because the
>> > mri_label2vol overlooks the index of 0, as the intensity value in the
>> > volumes starts with 1?
>> >
>> > I would appreciate your help on this.
>> >
>> > Leon
>> >
>> > *From:* Douglas N Greve > 

Re: [Freesurfer] Freesurfer-Error message

[Varghese Chikku]

Thanks Bruce,

Still no luck,this  what I am getting





/freesurfer/subjects/test1> recon-all -i
/media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm -subjid test7
-all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0

Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0

INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects

Actual FREESURFER_HOME /home/virtualuser/freesurfer Linux FreeSurfer
2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux

/home/virtualuser/freesurfer/subjects/test7



 mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm
/home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz



mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm
/home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz

file not found or unknown file type for file
/media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm

Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC
2009 i686 GNU/Linux



recon-all -s test7 exited with ERRORS at Wed Sep  5 09:51:17 EDT 2012



For more details, see the log file
/home/virtualuser/freesurfer/subjects/test7/scripts/recon-all.log

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



FreeSurfer:~/freesurfer/subjects/test1>


On 4 September 2012 14:37, Bruce Fischl  wrote:

> if that's the name of the image file. Can you post the list on your
> replies so others can answer?
>
> thanks
> Bruce
>
> On Tue, 4 Sep 2012, Varghese Chikku wrote:
>
> Hi Bruce,
>> Many thanks for  you mail.
>> Is this the  command  you referring to.
>> recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre/Image1.**dcm
>> -subjid test4
>> Thanks
>> Chikku
>>
>> On 3 September 2012 17:33, Bruce Fischl 
>> wrote:
>>   Hi Chikku
>>
>>   you need to give it the path to an image file (any one will do) and
>> it will figure out the other slices that makeup
>>   the same series. What is the resolution of your data? 50 slices
>> isn't usually enough to cover the brain at high
>>   enough resolution to get good thickness results.
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Mon, 3 Sep 2012, Varghese Chikku wrote:
>>
>>
>> Hi,
>>
>> While running the following command:
>>
>> recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre
>> -subjid test2
>>
>> I keep seeing the following error:
>>
>> ...
>>
>> corRead(): can't open file
>> /media/sf_freesurferstudys/**raw/raw_scr/T1pre/COR-.info
>> $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
>> reading from /media/sf_freesurferstudys/**
>> raw/raw_scr/T1pre...
>> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17
>> 01:57:59 UTC
>> 2009 i686 GNU/Linux
>> recon-all -s test2 exited with ERRORS at Fri Aug 31 04:20:28
>> EDT 2012
>>
>>
>> My image files, in dcm format, are at
>> /media/sf_freesurferstudys/**raw/raw_scr/T1pre :
>>
>> /media/sf_freesurferstudys/**raw/raw_scr/T1pre> ls
>> Image1  Image00010 Image00019  Image00028 Image00037
>> Image00046
>> Image2  Image00011 Image00020  Image00029 Image00038
>> Image00047
>> Image3  Image00012 Image00021  Image00030 Image00039
>> Image00048
>> Image4  Image00013 Image00022  Image00031 Image00040
>> Image00049
>> Image5  Image00014 Image00023  Image00032 Image00041
>> Image00050
>> Image6  Image00015 Image00024  Image00033 Image00042
>> Image7  Image00016 Image00025  Image00034 Image00043
>> Image8  Image00017 Image00026  Image00035 Image00044
>> Image9  Image00018 Image00027  Image00036 Image00045
>>
>>  Many thanks for  your help.
>> chikku
>>
>>
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/**complianceline.
>>  If the e-mail was sent to you in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
>>
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Re: [Freesurfer] Freesurfer-Error message

[Bruce Fischl]

Is that the actual name of the file? Does it have a dcm extension?
On Wed, 5 
Sep 2012, Varghese, Chikku wrote:

> Thanks Bruce,
> Still no luck,this  what I am getting
>
>
> /freesurfer/subjects/test1> recon-all -i 
> /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm -subjid test7 -all
> Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
> Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
> INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects
> Actual FREESURFER_HOME /home/virtualuser/freesurfer
> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 
> 2009 i686 GNU/Linux
> /home/virtualuser/freesurfer/subjects/test7
>
> mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm 
> /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz
>
> mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm 
> /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz
> file not found or unknown file type for file 
> /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm
> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 
> 2009 i686 GNU/Linux
>
> recon-all -s test7 exited with ERRORS at Wed Sep  5 09:51:17 EDT 2012
>
> For more details, see the log file 
> /home/virtualuser/freesurfer/subjects/test7/scripts/recon-all.log
> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> FreeSurfer:~/freesurfer/subjects/test1>
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Dienstag, 4. September 2012 18:25
> To: Varghese, Chikku
> Subject: Re: [Freesurfer] Freesurfer-Error message
>
> you need a -all at the end to tell it what to do. And please cc the list so 
> others can answer!
>
> On Tue, 4 Sep 2012, Varghese, Chikku wrote:
>
>>
>> recon-all -i
>> /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm -subjid
>> test4
>>
>> Is it this command I should use?
>>
>>
>>
>
>
> The information in this e-mail is intended only for the person to whom it is 
> addressed. If you believe this e-mail was sent to you in error and the e-mail 
> contains patient information, please contact the Partners Compliance HelpLine 
> at http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error but does not contain patient information, please contact the sender and 
> properly dispose of the e-mail.
>
>
>
>
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Re: [Freesurfer] FDR Correction of NHP Surface Data

[Douglas N Greve]

Hi Clark,  I just made a modification to mri_binarize to make it take an 
FDR as input. It computes the threshold and binarizes the input based on 
the threshold. I've put a copy here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize.linux

Run it with --help to get more info.

doug


On 08/29/2012 02:08 PM, Clark Fisher wrote:
> Hi Sebastian,
>
> I think you are right, both about tksurfer thresholding and the correct 
> interpretation of FDR. As you point out though, there is some value in having 
> maps that show how relatively well different points on the surface fit your 
> model.
>
> At the very least, is there any way to automate the retrieving of the 
> threshold that tksurfer provides? I'd still also be interested in some 
> adjustment to the whole map, if there's a way to do that as well.
>
> I could probably find a way to do this in Matlab, but I trust the 
> bug-squishing abilities of the freesurfer community more than I trust my own.
>
> -Clark
>
>
> On Aug 28, 2012, at 2:34 PM, Sebastian Moeller wrote:
>
>> Hi Clark,
>>
>>
>> On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote:
>>
>>> Hi Bruce,
>>>
>>> Thanks.  I actually have used this function of tksurfer, but am looking for 
>>> a way to save the corrected maps, so that they could be manipulated by 
>>> other tools (for instance, viewed by PySurfer).
>>  Does it really correct the map? I thought all it does is figure out the 
>> corrected threshold. By the way, if I understand correctly, FDR maps should 
>> be considered to be binary, that is you really do not know which voxels 
>> might be false positives, so you should not interpret all voxels to be 
>> equally significant. Having said that, almost everybody I know still looks 
>> at the p-value spatial distribution when looking at those FDR thresholded 
>> maps… (then again, I do not know any statistician...)
>>
>>
>> best
>>  Sebastian
>>
>>> I recognize that this may not be an officially supported functionality, but 
>>> is there some way to save the adjusted overlays from tksurfer, or create 
>>> them in some other way?
>>>
>>> Best,
>>> Clark
>>>
>>>
>>> On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote:
>>>
 Hi Clark

 you shouldn't need either. Load your overlays then click the button to 
 compute the FDR threshold in the tksurfer configure overlay interface.

 cheers
 Bruce
 On Tue, 28 Aug 2012, Clark Fisher wrote:

> Ok, maybe I'm making this question too intricate. Here's the short 
> version:
> How can I FDR correct painted surface significance maps when I have no 
> talraich .xfm file and no cortical segmentation?
> Thanks again,
> Clark
> Hi Freesurfers,
> I have another monkey-specific question.  I'd like to output 
> FDR-corrected signficance surface maps for my monkey data, or at least 
> FDR-threshold the maps.  It seems like mri_surfcluster might be one way 
> to go about this however:
>   1) I don't have any .xfm files for my monkeys, as I'm working in 
> native space, and
>   2) Without segmentation, I don't have a good mask to use for the 
> cortex only. My first attempts at work-arounds would be:
>   1)Try to create an identity .xfm file
>   2)Use the cortical ribbons from mris_volmask as a cortex mask
> Should these work?  If so, how should I make an identity .xfm file?  If 
> not, is there another way to FDR correct my surface data?
> Thanks,
> Clark
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> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
>>>
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>> -- 
>> Sebastian Moeller
>>
>> telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616
>> fax: 626-395-8826
>> German GSM:  +49 - 15 77 - 1 90 31 41
>> mobile:  +1-626-325-8598
>> +1-626-807-5242
>> US CDMA: +1-626-807-5242
>> moel...@caltech.edu
>>
>> Division of Biology
>> MC 114-96
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>> 1200 East California Boulevard
>> CA 91125, Pasadena
>> USA
>>
>
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>
>

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Douglas N

Re: [Freesurfer] mri_watershed and other errors.

[Darren Gitelman]

Nick, List:



Still no luck with this data. See attached as an example.



To get to this point I had run:



recon-all -all



This ran to the error: mri_watershed Error:   GLOBAL region of the brain
empty !



Then I followed your recommendation below



recon-all -s   -skullstrip -no-wsgcaatlas, which had no errors and
then

recon-all -s  -autorecon2 -autorecon3



This produced the result attached.



I then deleted this directory and re-imported all the dicom data for this
subject. Looked at the images, which look fine.

Then I ran recon-all -s  -autorecon1



This fails with the mri_watershed error.



Then I ran recon-all -s   -skullstrip -no-wsgcaatlas.



This runs without error but when I look at the brainmask.mgz it looks just
like the attached image.



Is there some way to set the thresholds differently? The T1 image looks
fine to me although perhaps the intensity is slightly less than usual, but
it doesn't seem particularly noisy.



Darren
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Re: [Freesurfer] resending question about 3rd level analysis

[Douglas N Greve]

Hi Susan, I've updated that web page to demonstrate how to run the 
random effects analysis. Let me know if that is clear or not.
doug

On 08/23/2012 12:38 PM, Susan Alice McLaughlin wrote:
> Hi,
>
> I'm resending this e-mail, as it didn't seem to go through correctly 
> yesterday:
>
> I’m a Freesurfer novice, and I’m confused about how to run a 3rd level 
> cross-subject analysis on the surface using as input cross-run .gfeats from 
> 10 subjects generated from a 2nd level analysis in FSL.
>
> Following the directions posted at 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat, I have 
> sampled the .gfeat copes and varcopes into standard surface space, using 
> mris_preproc.
>
> I would then go on to perform a 3rd level surface based analysis as the 
> instructions suggest, using:
>
> mri_glmfit --y xrun/lh.cope1.mgh --yffxvar xrun/lh.varcope1.mgh --ffxdof 163 
> --osgm --glmdir xrun/lh.osgm.ffx --surf fsaverage lh --label 
> $SUBJECTS_DIR/fsaverage/label/lh.cortex.label
>
> However, I want to use a random as opposed to fixed effects analysis. How do 
> I do this? I tried --yrfxvar as opposed to --yffxvar but it didn’t work. And 
> if I’m going to display the map resulting from this analysis, do I need to 
> correct for multiple comparisons?
>
> Many thanks in advance,
>
> Susan McLaughlin
> Doctoral Candidate
> SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex)
> Dept. of Speech and Hearing Sciences
> University of Washington
>
>
>
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] mris_anatomical_stats on multiple subjects

[Alexandra Tanner]

Hi again,

This is a follow-up question to my previous email -- the method I used may
not be the most efficient or the correct way to extract cortical thickness
from manually created ROIs. I'm unfamiliar with how to obtain thickness
data from a label, so I'm not sure if what I did is correct or if first I
must convert my label to volume or to an annotation file. If anyone knows
a better or more accurate way to measure thickness from the ROI I'd really
appreciate your advice!

Best,
Alex

> Hi Doug and Freesurfers,
>
> I'm currently working on extracting thickness measurements from an ROI I
manually created. I created my ROI label in tksurfer and applied the label
> to each subject I'd like to extract thickness data from using
> mri_label2label. I then used the following command to generate a stats
file, with the thickness measurement, from my label:
> mris_anatomical_stats  -f something.stats  -l something.label  subjid
?h
> (http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit).
>
> This generated a stats file that gave me the average thickness for my
ROI
> in my subject. I was wondering if there is a way to run the same
command,
> but on multiple subjects at once, so as not to have to run this command
on
> each individual subject. Any suggestions would be greatly appreciated!
>
> Best,
> Alex
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>
>





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Re: [Freesurfer] mri_watershed and other errors.

[Bruce Fischl]

Hi Darren

can you describe your input data? What format, resolution, etc... is it? 
If you upload it we'll take a look

cheers
Bruce
On Wed, 5 Sep 2012, Darren Gitelman 
wrote:




Nick, List:

 

Still no luck with this data. See attached as an example. 

 

To get to this point I had run:

 

recon-all -all 

 

This ran to the error: mri_watershed Error:   GLOBAL region of the brain empty !

 

Then I followed your recommendation below

 

recon-all -s   -skullstrip -no-wsgcaatlas, which had no errors and then

recon-all -s  -autorecon2 -autorecon3

 

This produced the result attached.

 

I then deleted this directory and re-imported all the dicom data for this 
subject. Looked at the images, which look fine.

Then I ran recon-all -s  -autorecon1

 

This fails with the mri_watershed error.

 

Then I ran recon-all -s   -skullstrip -no-wsgcaatlas.

 

This runs without error but when I look at the brainmask.mgz it looks just like 
the attached image.

 

Is there some way to set the thresholds differently? The T1 image looks fine to 
me although perhaps the intensity is slightly
less than usual, but it doesn't seem particularly noisy.

 

Darren

 


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Re: [Freesurfer] mri_watershed and other errors.

[Darren Gitelman]

Bruce:

Thank you for looking. I have uploaded the files:
I uploaded them in Dicom Format.
This is a T1, MPRAGE, image, acquired with GRAPPA, resolution 1x1x1.
Name: 3157.tar.gz

Darren



On Wed, Sep 5, 2012 at 11:27 AM, Bruce Fischl wrote:

> Hi Darren
>
> can you describe your input data? What format, resolution, etc... is it?
> If you upload it we'll take a look
> cheers
> Bruce
> On Wed, 5 Sep 2012, Darren Gitelman
> wrote:
>
> >
> > Nick, List:
> >
> >
> >
> > Still no luck with this data. See attached as an example.
> >
> >
> >
> > To get to this point I had run:
> >
> >
> >
> > recon-all -all
> >
> >
> >
> > This ran to the error: mri_watershed Error:   GLOBAL region of the brain
> empty !
> >
> >
> >
> > Then I followed your recommendation below
> >
> >
> >
> > recon-all -s   -skullstrip -no-wsgcaatlas, which had no errors
> and then
> >
> > recon-all -s  -autorecon2 -autorecon3
> >
> >
> >
> > This produced the result attached.
> >
> >
> >
> > I then deleted this directory and re-imported all the dicom data for
> this subject. Looked at the images, which look fine.
> >
> > Then I ran recon-all -s  -autorecon1
> >
> >
> >
> > This fails with the mri_watershed error.
> >
> >
> >
> > Then I ran recon-all -s   -skullstrip -no-wsgcaatlas.
> >
> >
> >
> > This runs without error but when I look at the brainmask.mgz it looks
> just like the attached image.
> >
> >
> >
> > Is there some way to set the thresholds differently? The T1 image looks
> fine to me although perhaps the intensity is slightly
> > less than usual, but it doesn't seem particularly noisy.
> >
> >
> >
> > Darren
> >
> >
> >
> >
> >
>
>
> 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.
>



-- 
Darren Gitelman, MD
Northwestern University
710 N. Lake Shore Dr.
Abbott 11th Floor
Chicago, IL 60611
Ph: (312) 908-8614
Fax: (312) 908-5073
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Re: [Freesurfer] creating a gca file from .mgz files

[Jeff Thompson]

Hello,
I got mri_ca_train to complete and to produce a .gca file, which looks to be 
what is expected after splitting it up into means/labels/priors files. 
The problem was the norm.mgz file. I ended up copying and renaming the T1.mgz 
file to replace the norm.mgz file, and it seemed to work in mri_ca_train.
I am now having trouble with the aseg.mgz file in mri_normalize. It states that 
the aseg.mgz file needs to be conformed. When I conform the image the label 
values are way off. I tried the mri_convert 
conform with the rt nearest , but the label values seemed to still be off.
The file I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90.   
Any recommendations to solve this problem?
Thank you,

Jeff Thompson


> Subject: Re: [Freesurfer] creating a gca file from .mgz files
> From: ni...@nmr.mgh.harvard.edu
> To: jeff_rthomp...@hotmail.com
> CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
> Date: Wed, 29 Aug 2012 19:56:09 -0400
> 
> i think there should be an error log that outputs the errors that
> mri_ca_train found.  or you can run mri_ca_train with the -check flag.
> it performs checks looking for voxels that are in the wrong hemisphere,
> based on the talairach registration.
> 
> for mri_convert, be sure to include the flag 
> 
> -rt nearest
> 
> which overrides the default resample type of 'interpolate', which is not
> appropriate for labeled volumes.
> 
> n.
> 
> 
> On Wed, 2012-08-29 at 18:20 -0300, Jeff Thompson wrote:
> > Hello,
> > 
> > 
> > Still getting the bus error when running mri_ca_train. I tried running
> > it after I conformed the manually labelled volume as well.
> > 
> > 
> > I've been working on getting rebuild_gca_atlas.csh to work. I don't
> > know how to get the labelled volume to conform when converting the
> > labelled volume to .mgz with mri_convert without throwing all of the
> > label values off. 
> > 
> > 
> > This resulted in a lot of errors when running rebuild_gca_atlas.csh
> > and gave an error stating 
> > 
> > 
> > "ERROR: mri_ca_train check found 1 subjects with bad labels!"
> > 
> > 
> > 
> > 
> > Thanks,
> > 
> > Jeff Thompson
> > 
> > 
> > 
> > 
> > 
> > __
> > CC: freesurfer@nmr.mgh.harvard.edu
> > From: fis...@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] creating a gca file from .mgz files
> > Date: Tue, 28 Aug 2012 20:12:45 -0400
> > To: jeff_rthomp...@hotmail.com
> > 
> > Oh, so you still got a bus error? I didn't realize that. Make sure the
> > seg volumes are ok
> > 
> > 
> > 
> > 
> > On Aug 28, 2012, at 6:10 PM, Jeff Thompson
> >  wrote:
> > 
> > 
> > 
> > Hopefully that doesn't scale the values I will make sure it
> > doesn't. 
> > 
> > 
> > When running mri_ca_train by itself after changing to float
> > the next error was the Bus error.
> > 
> > 
> > When running rebuild_gca_atlas.csh I was having problems with
> > pbsubmit, but after avoiding that it seems to be stuck with
> > mri_ca_train.
> > 
> > 
> > 
> > 
> > 
> > 
> > > Date: Tue, 28 Aug 2012 17:02:51 -0400
> > > From: fis...@nmr.mgh.harvard.edu
> > > To: jeff_rthomp...@hotmail.com
> > > CC: freesurfer@nmr.mgh.harvard.edu
> > > Subject: RE: [Freesurfer] creating a gca file from .mgz
> > files
> > > 
> > > does that scale the values? Hopefully not. It sounds like
> > things don't fail 
> > > after you changed to float until you get the pbsubmit
> > problem, correct?
> > > 
> > > On Tue, 28 Aug 2012, Jeff Thompson wrote:
> > > 
> > > > To change to type Float I used:  
> > > > fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0
> > > > Alloybrain_mask_LUTComplete_float.nii.gz -odt float
> > > > 
> > > > I will try some other methods for changing the data type,
> > but if that isn't
> > > > the issue are there other cases of getting similar errors
> > from mri_ca_train?
> > > > 
> > > > thanks,
> > > > 
> > > > Jeff
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > > Date: Tue, 28 Aug 2012 16:37:19 -0400
> > > > > From: fis...@nmr.mgh.harvard.edu
> > > > > To: jeff_rthomp...@hotmail.com
> > > > > CC: freesurfer@nmr.mgh.harvard.edu
> > > > > Subject: RE: [Freesurfer] creating a gca file from .mgz
> > files
> > > > >
> > > > > how did you change the type to float? Make sure it
> > doesn't scale the
> > > > > inputs if that is the segmentation volume.
> > rebuild_gca_atlas.csh uses our
> > > > > compute cluster queueing system which is what the
> > pbsubmit script is.
> > > > > You'll need to mo

Re: [Freesurfer] Repost: Converting BV ROIs to FS

[Katie Bettencourt]

Ok,  I am trying to use the select_talairach_point command, and I have it
in part of a script that uses tksurfer to load up a subject's inflated
surface, load the curvature, and load an overlay, but it doesn't seem to be
doing anything.  Is there a step I am missing?  What should I see if it
works correctly?

Thanks for all your help!
Katie

On Wed, Sep 5, 2012 at 9:19 AM, Bruce Fischl wrote:

> Hi Katie
>
> you can view data on a  tal brain by mapping the data using the
> talairach.xfm transform. Since you can also use the inverse of the
> transform you can map both ways. I think there is a tcl command in tksurfer
> for finding the vertex that is closest to a given tal coord. Try:
>
> select_talairach_point   
>
> cheers
>
> Bruce
>
>
> On Tue, 4 Sep 2012, Katie Bettencourt wrote:
>
>  Hrm.  Ok, is there any way to view data for a subject in Freesurfer on a
>> talairach transformed brain? What I would be hoping to do is bring up the
>> data in native subject space, make any ROI label, then also bring the data
>> up on a talairach transformed brain, make a ROI label, then put both
>> labels
>> on the same brain (either native or talairach transformed) and see if they
>> are any different.
>> Also, is there a way to input a particular talairach vertex and jump to
>> that
>> in freesurfer, instead of just moving the mouse around and hoping to find
>> the right spot?
>>
>> Katie
>>
>> On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl > >
>> wrote:
>>   Hi Katie
>>
>>   I don't think anyone here knows how to do this as we don't use
>>   it. Perhaps the Brain Voyager people do?
>>
>>   sorry,
>>   Bruce
>>   On Tue, 4 Sep 2012, Katie Bettencourt wrote:
>>
>>
>>   So our lab is running a couple analyses and we
>> are getting different results based on whether we
>> use Brain Voyager or
>>   Freesurfer that we think is due to different
>> ROI selection across the two platforms.  Is there
>> anyway to load a
>>   BrainVoyager ROI into freesurfer?  The BV data
>> has been talairach transformed, does that matter?
>>  Less optimal would
>>   be loading a freesurfer ROI into BV, but if
>> that's easier, we could try that way too.
>> Any help would be appreciated.
>>
>> Katie
>>
>>
>>
>>
>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/**complianceline.
>>  If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
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Re: [Freesurfer] creating a gca file from .mgz files

[Douglas N Greve]

I don't think you actually want to do the full conformation as that will 
change the type to uchar, which is probably what is messing up your 
values. Instead, try this

mri_vol2vol --mov aseg.mgz --targ orig.mgz --regheader --interp nearest 
--precision int --o aseg.conf.mgz

doug


On 09/05/2012 12:47 PM, Jeff Thompson wrote:
> Hello,
>
> I got mri_ca_train to complete and to produce a .gca file, which looks 
> to be what is expected after splitting it up into means/labels/priors 
> files.
>
> The problem was the norm.mgz file. I ended up copying and renaming the 
> T1.mgz file to replace the norm.mgz file, and it seemed to work in 
> mri_ca_train.
>
> I am now having trouble with the aseg.mgz file in mri_normalize. It 
> states that the aseg.mgz file needs to be conformed. When I conform 
> the image the label values are way off. I tried the mri_convert
>
> conform with the rt nearest , but the label values seemed to still be off.
>
> The file I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90.
>
> Any recommendations to solve this problem?
>
> Thank you,
>
> Jeff Thompson
>
>
> > Subject: Re: [Freesurfer] creating a gca file from .mgz files
> > From: ni...@nmr.mgh.harvard.edu
> > To: jeff_rthomp...@hotmail.com
> > CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
> > Date: Wed, 29 Aug 2012 19:56:09 -0400
> >
> > i think there should be an error log that outputs the errors that
> > mri_ca_train found. or you can run mri_ca_train with the -check flag.
> > it performs checks looking for voxels that are in the wrong hemisphere,
> > based on the talairach registration.
> >
> > for mri_convert, be sure to include the flag
> >
> > -rt nearest
> >
> > which overrides the default resample type of 'interpolate', which is not
> > appropriate for labeled volumes.
> >
> > n.
> >
> >
> > On Wed, 2012-08-29 at 18:20 -0300, Jeff Thompson wrote:
> > > Hello,
> > >
> > >
> > > Still getting the bus error when running mri_ca_train. I tried running
> > > it after I conformed the manually labelled volume as well.
> > >
> > >
> > > I've been working on getting rebuild_gca_atlas.csh to work. I don't
> > > know how to get the labelled volume to conform when converting the
> > > labelled volume to .mgz with mri_convert without throwing all of the
> > > label values off.
> > >
> > >
> > > This resulted in a lot of errors when running rebuild_gca_atlas.csh
> > > and gave an error stating
> > >
> > >
> > > "ERROR: mri_ca_train check found 1 subjects with bad labels!"
> > >
> > >
> > >
> > >
> > > Thanks,
> > >
> > > Jeff Thompson
> > >
> > >
> > >
> > >
> > >
> > > __
> > > CC: freesurfer@nmr.mgh.harvard.edu
> > > From: fis...@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] creating a gca file from .mgz files
> > > Date: Tue, 28 Aug 2012 20:12:45 -0400
> > > To: jeff_rthomp...@hotmail.com
> > >
> > > Oh, so you still got a bus error? I didn't realize that. Make sure the
> > > seg volumes are ok
> > >
> > >
> > >
> > >
> > > On Aug 28, 2012, at 6:10 PM, Jeff Thompson
> > >  wrote:
> > >
> > >
> > >
> > > Hopefully that doesn't scale the values I will make sure it
> > > doesn't.
> > >
> > >
> > > When running mri_ca_train by itself after changing to float
> > > the next error was the Bus error.
> > >
> > >
> > > When running rebuild_gca_atlas.csh I was having problems with
> > > pbsubmit, but after avoiding that it seems to be stuck with
> > > mri_ca_train.
> > >
> > >
> > >
> > >
> > >
> > >
> > > > Date: Tue, 28 Aug 2012 17:02:51 -0400
> > > > From: fis...@nmr.mgh.harvard.edu
> > > > To: jeff_rthomp...@hotmail.com
> > > > CC: freesurfer@nmr.mgh.harvard.edu
> > > > Subject: RE: [Freesurfer] creating a gca file from .mgz
> > > files
> > > >
> > > > does that scale the values? Hopefully not. It sounds like
> > > things don't fail
> > > > after you changed to float until you get the pbsubmit
> > > problem, correct?
> > > >
> > > > On Tue, 28 Aug 2012, Jeff Thompson wrote:
> > > >
> > > > > To change to type Float I used:
> > > > > fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0
> > > > > Alloybrain_mask_LUTComplete_float.nii.gz -odt float
> > > > >
> > > > > I will try some other methods for changing the data type,
> > > but if that isn't
> > > > > the issue are there other cases of getting similar errors
> > > from mri_ca_train?
> > > > >
> > > > > thanks,
> > > > >
> > > > > Jeff
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > > Date: Tue, 28 Aug 2012 16:37:19 -0400
> > > > > > From: fis...@nmr.mgh.harvard.edu
> > > > > > To: jeff_rthomp...@hotmail.com
> > > > > > CC: freesurfer@nmr.mgh.harvard.edu
> > > > > > Subject: RE: [Freesurfer] creating a gca file from .mgz
> > > files
> > > > > >
> > > > > > how did you change the type to float? Make sure it
> > > doesn't scale the
> > > > > > inputs if that is the segmentation volume.
> > > rebuild_gca_atlas.csh uses our
> > > > > > compute cluster queueing system which

Re: [Freesurfer] creating a gca file from .mgz files

[Bruce Fischl]

what is your mri_convert command line?

On Wed, 5 Sep 2012, Jeff Thompson wrote:


Hello,
I got mri_ca_train to complete and to produce a .gca file, which looks to be
what is expected after splitting it up into means/labels/priors files. 

The problem was the norm.mgz file. I ended up copying and renaming the
T1.mgz file to replace the norm.mgz file, and it seemed to work in
mri_ca_train.

I am now having trouble with the aseg.mgz file in mri_normalize. It states
that the aseg.mgz file needs to be conformed. When I conform the image the
label values are way off. I tried the mri_convert 

conform with the rt nearest , but the label values seemed to still be off.

The file I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90.   

Any recommendations to solve this problem?

Thank you,

Jeff Thompson


> Subject: Re: [Freesurfer] creating a gca file from .mgz files
> From: ni...@nmr.mgh.harvard.edu
> To: jeff_rthomp...@hotmail.com
> CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
> Date: Wed, 29 Aug 2012 19:56:09 -0400
>
> i think there should be an error log that outputs the errors that
> mri_ca_train found. or you can run mri_ca_train with the -check flag.
> it performs checks looking for voxels that are in the wrong hemisphere,
> based on the talairach registration.
>
> for mri_convert, be sure to include the flag
>
> -rt nearest
>
> which overrides the default resample type of 'interpolate', which is not
> appropriate for labeled volumes.
>
> n.
>
>
> On Wed, 2012-08-29 at 18:20 -0300, Jeff Thompson wrote:
> > Hello,
> >
> >
> > Still getting the bus error when running mri_ca_train. I tried running
> > it after I conformed the manually labelled volume as well.
> >
> >
> > I've been working on getting rebuild_gca_atlas.csh to work. I don't
> > know how to get the labelled volume to conform when converting the
> > labelled volume to .mgz with mri_convert without throwing all of the
> > label values off.
> >
> >
> > This resulted in a lot of errors when running rebuild_gca_atlas.csh
> > and gave an error stating
> >
> >
> > "ERROR: mri_ca_train check found 1 subjects with bad labels!"
> >
> >
> >
> >
> > Thanks,
> >
> > Jeff Thompson
> >
> >
> >
> >
> >
> > __
> > CC: freesurfer@nmr.mgh.harvard.edu
> > From: fis...@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] creating a gca file from .mgz files
> > Date: Tue, 28 Aug 2012 20:12:45 -0400
> > To: jeff_rthomp...@hotmail.com
> >
> > Oh, so you still got a bus error? I didn't realize that. Make sure the
> > seg volumes are ok
> >
> >
> >
> >
> > On Aug 28, 2012, at 6:10 PM, Jeff Thompson
> >  wrote:
> >
> >
> >
> > Hopefully that doesn't scale the values I will make sure it
> > doesn't.
> >
> >
> > When running mri_ca_train by itself after changing to float
> > the next error was the Bus error.
> >
> >
> > When running rebuild_gca_atlas.csh I was having problems with
> > pbsubmit, but after avoiding that it seems to be stuck with
> > mri_ca_train.
> >
> >
> >
> >
> >
> >
> > > Date: Tue, 28 Aug 2012 17:02:51 -0400
> > > From: fis...@nmr.mgh.harvard.edu
> > > To: jeff_rthomp...@hotmail.com
> > > CC: freesurfer@nmr.mgh.harvard.edu
> > > Subject: RE: [Freesurfer] creating a gca file from .mgz
> > files
> > >
> > > does that scale the values? Hopefully not. It sounds like
> > things don't fail
> > > after you changed to float until you get the pbsubmit
> > problem, correct?
> > >
> > > On Tue, 28 Aug 2012, Jeff Thompson wrote:
> > >
> > > > To change to type Float I used:
> > > > fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0
> > > > Alloybrain_mask_LUTComplete_float.nii.gz -odt float
> > > >
> > > > I will try some other methods for changing the data type,
> > but if that isn't
> > > > the issue are there other cases of getting similar errors
> > from mri_ca_train?
> > > >
> > > > thanks,
> > > >
> > > > Jeff
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > > Date: Tue, 28 Aug 2012 16:37:19 -0400
> > > > > From: fis...@nmr.mgh.harvard.edu
> > > > > To: jeff_rthomp...@hotmail.com
> > > > > CC: freesurfer@nmr.mgh.harvard.edu
> > > > > Subject: RE: [Freesurfer] creating a gca file from .mgz
> > files
> > > > >
> > > > > how did you change the type to float? Make sure it
> > doesn't scale the
> > > > > inputs if that is the segmentation volume.
> > rebuild_gca_atlas.csh uses our
> > > > > compute cluster queueing system which is what the
> > pbsubmit script is.
> > > > > You'll need to modify it to use whatever cluster you are
> > using or to run
> > > > > them in series
> > > > >
> > > > > cheers
> > > > > Bruce
> > > > > On Tue, 28 Aug 2012, Jeff Thompson wrote:
> > > > >
> > > > > >
> > > > > > Hello,
> > > > > > When running the mri_ca_train I am getting a Bus error
> > near the
> > > > beginning of
> > > > > > it.
> > > > > >
> > > > > > 'bash-3.2$ mri_ca_train -parc_dir
> > Alloybrain_mask_LUTComplete_float.mgz
> > > > -T1
> > > > > > norm.mgz Alloy single_on

Re: [Freesurfer] Covary for categorical variable in QDEC

[Douglas N Greve]

Hi Jeff, sorry, what do you mean to covary for a categorical variable?
doug

On 09/05/2012 12:43 AM, Jeff Sadino wrote:
> Hello,
>
> Is it possible to covary for a categorical variable in QDEC?  I see 
> other posters have said it is not possible, but I did not see 
> any official documentation or response regarding the issue.
>
> Thank You,
> Jeff Sadino
>
>
>
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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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Re: [Freesurfer] Repost: Converting BV ROIs to FS

[Katie Bettencourt]

Nevermind, it turns out it was due to an permissions error.

Thanks again.

Katie

On Wed, Sep 5, 2012 at 12:53 PM, Katie Bettencourt wrote:

> Ok,  I am trying to use the select_talairach_point command, and I have it
> in part of a script that uses tksurfer to load up a subject's inflated
> surface, load the curvature, and load an overlay, but it doesn't seem to be
> doing anything.  Is there a step I am missing?  What should I see if it
> works correctly?
>
> Thanks for all your help!
> Katie
>
>
> On Wed, Sep 5, 2012 at 9:19 AM, Bruce Fischl 
> wrote:
>
>> Hi Katie
>>
>> you can view data on a  tal brain by mapping the data using the
>> talairach.xfm transform. Since you can also use the inverse of the
>> transform you can map both ways. I think there is a tcl command in tksurfer
>> for finding the vertex that is closest to a given tal coord. Try:
>>
>> select_talairach_point   
>>
>> cheers
>>
>> Bruce
>>
>>
>> On Tue, 4 Sep 2012, Katie Bettencourt wrote:
>>
>>  Hrm.  Ok, is there any way to view data for a subject in Freesurfer on a
>>> talairach transformed brain? What I would be hoping to do is bring up the
>>> data in native subject space, make any ROI label, then also bring the
>>> data
>>> up on a talairach transformed brain, make a ROI label, then put both
>>> labels
>>> on the same brain (either native or talairach transformed) and see if
>>> they
>>> are any different.
>>> Also, is there a way to input a particular talairach vertex and jump to
>>> that
>>> in freesurfer, instead of just moving the mouse around and hoping to find
>>> the right spot?
>>>
>>> Katie
>>>
>>> On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>   Hi Katie
>>>
>>>   I don't think anyone here knows how to do this as we don't use
>>>   it. Perhaps the Brain Voyager people do?
>>>
>>>   sorry,
>>>   Bruce
>>>   On Tue, 4 Sep 2012, Katie Bettencourt wrote:
>>>
>>>
>>>   So our lab is running a couple analyses and we
>>> are getting different results based on whether we
>>> use Brain Voyager or
>>>   Freesurfer that we think is due to different
>>> ROI selection across the two platforms.  Is there
>>> anyway to load a
>>>   BrainVoyager ROI into freesurfer?  The BV data
>>> has been talairach transformed, does that matter?
>>>  Less optimal would
>>>   be loading a freesurfer ROI into BV, but if
>>> that's easier, we could try that way too.
>>> Any help would be appreciated.
>>>
>>> Katie
>>>
>>>
>>>
>>>
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/**complianceline.
>>>  If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender
>>> and properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>
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Re: [Freesurfer] mri_watershed and other errors.

[Nick Schmansky]

Darren,

I forgot to mention that you'll need to add 

-clean-bm

after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be
retained and the new one will be saved as brainmask.auto.mgz.

Nick


On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
> Nick, List:
> 
>  
> 
> Still no luck with this data. See attached as an example. 
> 
>  
> 
> To get to this point I had run:
> 
>  
> 
> recon-all -all 
> 
>  
> 
> This ran to the error: mri_watershed Error:   GLOBAL region of the
> brain empty !
> 
>  
> 
> Then I followed your recommendation below
> 
>  
> 
> recon-all -s   -skullstrip -no-wsgcaatlas, which had no errors
> and then
> 
> recon-all -s  -autorecon2 -autorecon3
> 
>  
> 
> This produced the result attached.
> 
>  
> 
> I then deleted this directory and re-imported all the dicom data for
> this subject. Looked at the images, which look fine.
> 
> Then I ran recon-all -s  -autorecon1
> 
>  
> 
> This fails with the mri_watershed error.
> 
>  
> 
> Then I ran recon-all -s   -skullstrip -no-wsgcaatlas.
> 
>  
> 
> This runs without error but when I look at the brainmask.mgz it looks
> just like the attached image.
> 
>  
> 
> Is there some way to set the thresholds differently? The T1 image
> looks fine to me although perhaps the intensity is slightly less than
> usual, but it doesn't seem particularly noisy.
> 
>  
> 
> Darren
> 
>  
> 
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Re: [Freesurfer] tksurfer not working properly

[Nick Schmansky]

Deirdre,

this is the infamous 'sliver' problem.  consult this page for solutions:

https://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems

Nick



On Wed, 2012-09-05 at 13:39 -0400, Deirdre O Shea wrote:
> Hello,
> 
> I am just getting to get grips with using FreeSurfer to reconstruct
> images, however, any time I try to load tksurfer it only displays a
> very small part of the image (see attached for what i mean). I was
> hoping someone could give me an explanation as to why this may be
> happening and whether there is a solution to fixing it.
> 
> Best Deirdre
> 
> 
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[Freesurfer] Covary for a categorical variable in mri_glmfit

[Jeff Sadino]

Hello,

I am trying to covary for Gender in mri_glmfit, but I am having errors pop
up.  I tried to follow Doug's suggesting in this post:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html
but after modifying my Xg.dat file and rerunning mri_glmfit, it says:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1.53319e+07

I can run it using the --illcond flag, but then I get a bunch of:
***
CEPHES ERROR: fdtrc domain error
***

Can anyone please give advice on how to covary for Gender in mri_glmfit (or
qdec)?

As always, thank you for all of your great help!!
Jeff Sadino
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Re: [Freesurfer] Covary for a categorical variable in mri_glmfit

[Douglas N Greve]

I still don't know what you mean by covarying for gender. What is your 
design? Can you send your FSGD file?
doug

On 09/05/2012 04:44 PM, Jeff Sadino wrote:
> Hello,
>
> I am trying to covary for Gender in mri_glmfit, but I am having errors 
> pop up.  I tried to follow Doug's suggesting in this post:
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html
> but after modifying my Xg.dat file and rerunning mri_glmfit, it says:
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1.53319e+07
>
> I can run it using the --illcond flag, but then I get a bunch of:
> ***
> CEPHES ERROR: fdtrc domain error
> ***
>
> Can anyone please give advice on how to covary for Gender in 
> mri_glmfit (or qdec)?
>
> As always, thank you for all of your great help!!
> Jeff Sadino
>
>
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Re: [Freesurfer] mri_watershed and other errors.

[Bruce Fischl]

I'm running it now with the current dev version and it's passed the skull 
stripping stage and it seems to have worked fine...

On Wed, 
5 Sep 2012, Nick Schmansky wrote:

> Darren,
>
> I forgot to mention that you'll need to add
>
> -clean-bm
>
> after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be
> retained and the new one will be saved as brainmask.auto.mgz.
>
> Nick
>
>
> On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
>> Nick, List:
>>
>>
>>
>> Still no luck with this data. See attached as an example.
>>
>>
>>
>> To get to this point I had run:
>>
>>
>>
>> recon-all -all
>>
>>
>>
>> This ran to the error: mri_watershed Error:   GLOBAL region of the
>> brain empty !
>>
>>
>>
>> Then I followed your recommendation below
>>
>>
>>
>> recon-all -s   -skullstrip -no-wsgcaatlas, which had no errors
>> and then
>>
>> recon-all -s  -autorecon2 -autorecon3
>>
>>
>>
>> This produced the result attached.
>>
>>
>>
>> I then deleted this directory and re-imported all the dicom data for
>> this subject. Looked at the images, which look fine.
>>
>> Then I ran recon-all -s  -autorecon1
>>
>>
>>
>> This fails with the mri_watershed error.
>>
>>
>>
>> Then I ran recon-all -s   -skullstrip -no-wsgcaatlas.
>>
>>
>>
>> This runs without error but when I look at the brainmask.mgz it looks
>> just like the attached image.
>>
>>
>>
>> Is there some way to set the thresholds differently? The T1 image
>> looks fine to me although perhaps the intensity is slightly less than
>> usual, but it doesn't seem particularly noisy.
>>
>>
>>
>> Darren
>>
>>
>>
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>
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>
>
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Re: [Freesurfer] mri_watershed and other errors.

[Darren Gitelman]

Bruce

I used the following
version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522

Is that the same as the one you are using or are you referring to an
internal development version?

I will try Nick's suggestion as well.

Darren

On Wed, Sep 5, 2012 at 4:05 PM, Bruce Fischl wrote:

> I'm running it now with the current dev version and it's passed the skull
> stripping stage and it seems to have worked fine...
>
> On Wed,
> 5 Sep 2012, Nick Schmansky wrote:
>
> > Darren,
> >
> > I forgot to mention that you'll need to add
> >
> > -clean-bm
> >
> > after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be
> > retained and the new one will be saved as brainmask.auto.mgz.
> >
> > Nick
> >
> >
> > On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
> >> Nick, List:
> >>
> >>
> >>
> >> Still no luck with this data. See attached as an example.
> >>
> >>
> >>
> >> To get to this point I had run:
> >>
> >>
> >>
> >> recon-all -all
> >>
> >>
> >>
> >> This ran to the error: mri_watershed Error:   GLOBAL region of the
> >> brain empty !
> >>
> >>
> >>
> >> Then I followed your recommendation below
> >>
> >>
> >>
> >> recon-all -s   -skullstrip -no-wsgcaatlas, which had no errors
> >> and then
> >>
> >> recon-all -s  -autorecon2 -autorecon3
> >>
> >>
> >>
> >> This produced the result attached.
> >>
> >>
> >>
> >> I then deleted this directory and re-imported all the dicom data for
> >> this subject. Looked at the images, which look fine.
> >>
> >> Then I ran recon-all -s  -autorecon1
> >>
> >>
> >>
> >> This fails with the mri_watershed error.
> >>
> >>
> >>
> >> Then I ran recon-all -s   -skullstrip -no-wsgcaatlas.
> >>
> >>
> >>
> >> This runs without error but when I look at the brainmask.mgz it looks
> >> just like the attached image.
> >>
> >>
> >>
> >> Is there some way to set the thresholds differently? The T1 image
> >> looks fine to me although perhaps the intensity is slightly less than
> >> usual, but it doesn't seem particularly noisy.
> >>
> >>
> >>
> >> Darren
> >>
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the 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.
>
>


-- 
Darren Gitelman, MD
Northwestern University
710 N. Lake Shore Dr.
Abbott 11th Floor
Chicago, IL 60611
Ph: (312) 908-8614
Fax: (312) 908-5073
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Re: [Freesurfer] mri_watershed and other errors.

[Darren Gitelman]

Nick

I ran:  recon-all -skullstrip -no-wsgcaatlas -clean-bm -s 3157

and got the exact same problem with brainmask.mgz

Darren

On Wed, Sep 5, 2012 at 3:37 PM, Nick Schmansky wrote:

> Darren,
>
> I forgot to mention that you'll need to add
>
> -clean-bm
>
> after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be
> retained and the new one will be saved as brainmask.auto.mgz.
>
> Nick
>
>
> On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
> > Nick, List:
> >
> >
> >
> > Still no luck with this data. See attached as an example.
> >
> >
> >
> > To get to this point I had run:
> >
> >
> >
> > recon-all -all
> >
> >
> >
> > This ran to the error: mri_watershed Error:   GLOBAL region of the
> > brain empty !
> >
> >
> >
> > Then I followed your recommendation below
> >
> >
> >
> > recon-all -s   -skullstrip -no-wsgcaatlas, which had no errors
> > and then
> >
> > recon-all -s  -autorecon2 -autorecon3
> >
> >
> >
> > This produced the result attached.
> >
> >
> >
> > I then deleted this directory and re-imported all the dicom data for
> > this subject. Looked at the images, which look fine.
> >
> > Then I ran recon-all -s  -autorecon1
> >
> >
> >
> > This fails with the mri_watershed error.
> >
> >
> >
> > Then I ran recon-all -s   -skullstrip -no-wsgcaatlas.
> >
> >
> >
> > This runs without error but when I look at the brainmask.mgz it looks
> > just like the attached image.
> >
> >
> >
> > Is there some way to set the thresholds differently? The T1 image
> > looks fine to me although perhaps the intensity is slightly less than
> > usual, but it doesn't seem particularly noisy.
> >
> >
> >
> > Darren
> >
> >
> >
> > ___
> > 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.
>



-- 
Darren Gitelman, MD
Northwestern University
710 N. Lake Shore Dr.
Abbott 11th Floor
Chicago, IL 60611
Ph: (312) 908-8614
Fax: (312) 908-5073
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Re: [Freesurfer] mri_watershed and other errors.

[Bruce Fischl]

our internal development version.
On Wed, 5 Sep 2012, Darren Gitelman 
wrote:



Bruce
I used the following
version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522

Is that the same as the one you are using or are you referring to an
internal development version?

I will try Nick's suggestion as well.

Darren

On Wed, Sep 5, 2012 at 4:05 PM, Bruce Fischl 
wrote:
  I'm running it now with the current dev version and it's passed
  the skull
  stripping stage and it seems to have worked fine...

  On Wed,
  5 Sep 2012, Nick Schmansky wrote:

  > Darren,
  >
  > I forgot to mention that you'll need to add
  >
  > -clean-bm
  >
  > after the -no-wsgcaatlas flag, otherwise the prior
  brainmask.mgz will be
  > retained and the new one will be saved as brainmask.auto.mgz.
  >
  > Nick
  >
  >
  > On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
>> Nick, List:
>>
>>
>>
>> Still no luck with this data. See attached as an example.
>>
>>
>>
>> To get to this point I had run:
>>
>>
>>
>> recon-all -all
>>
>>
>>
>> This ran to the error: mri_watershed Error:   GLOBAL region of the
>> brain empty !
>>
>>
>>
>> Then I followed your recommendation below
>>
>>
>>
>> recon-all -s   -skullstrip -no-wsgcaatlas, which had no
errors
>> and then
>>
>> recon-all -s  -autorecon2 -autorecon3
>>
>>
>>
>> This produced the result attached.
>>
>>
>>
>> I then deleted this directory and re-imported all the dicom data
for
>> this subject. Looked at the images, which look fine.
>>
>> Then I ran recon-all -s  -autorecon1
>>
>>
>>
>> This fails with the mri_watershed error.
>>
>>
>>
>> Then I ran recon-all -s   -skullstrip -no-wsgcaatlas.
>>
>>
>>
>> This runs without error but when I look at the brainmask.mgz it
looks
>> just like the attached image.
>>
>>
>>
>> Is there some way to set the thresholds differently? The T1 image
>> looks fine to me although perhaps the intensity is slightly less
than
>> usual, but it doesn't seem particularly noisy.
>>
>>
>>
>> Darren
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>


The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
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in error
but does not contain patient information, please contact the sender
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dispose of the e-mail.




--
Darren Gitelman, MD
Northwestern University
710 N. Lake Shore Dr.
Abbott 11th Floor
Chicago, IL 60611
Ph: (312) 908-8614
Fax: (312) 908-5073



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Re: [Freesurfer] Covary for a categorical variable in mri_glmfit

[Jeff Sadino]

Hello,

I think our emails were getting crossed in cyberspace.  I have a group that
has a disproportionate number of females, and so there is a significant
difference in the number of females as compared to males (chi-square
p=.01).  This must be accounted for.  If I find that one group has a
smaller brain volume, etc., then it could be attributed to one group having
fewer females than the others.  My ultimate goal is to run an analysis on
the thickness, taking into account these sex differences (and ICV and age).
 My plan was to covary for sex, icv, and age.  I have covaried for icv and
age lots of times, but I am having trouble covarying (if that is the right
word) for this categorical sex variable.

Any help would be greatly appreciated!
Jeff

On Wed, Sep 5, 2012 at 10:44 AM, Jeff Sadino wrote:

> Hello,
>
> I am trying to covary for Gender in mri_glmfit, but I am having errors pop
> up.  I tried to follow Doug's suggesting in this post:
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html
> but after modifying my Xg.dat file and rerunning mri_glmfit, it says:
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1.53319e+07
>
> I can run it using the --illcond flag, but then I get a bunch of:
> ***
> CEPHES ERROR: fdtrc domain error
> ***
>
> Can anyone please give advice on how to covary for Gender in mri_glmfit
> (or qdec)?
>
> As always, thank you for all of your great help!!
> Jeff Sadino
>
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Re: [Freesurfer] Covary for a categorical variable in mri_glmfit

[Douglas Greve]

Use gender as a discrete variable in the FSGD, ie, a class for M and a 
class for F. If you have two other groups (say, normals and patients), 
then use four classes (Mnormals, Mpatients, etc). Then test for the 
normals vs patients with (Mnorm+Fnorm) - (Mpat+Fpat). This "regresses 
out" gender.

doug

On 9/5/12 8:10 PM, Jeff Sadino wrote:

Hello,

I think our emails were getting crossed in cyberspace.  I have a group 
that has a disproportionate number of females, and so there is a 
significant difference in the number of females as compared to males 
(chi-square p=.01).  This must be accounted for.  If I find that one 
group has a smaller brain volume, etc., then it could be attributed to 
one group having fewer females than the others.  My ultimate goal is 
to run an analysis on the thickness, taking into account these sex 
differences (and ICV and age).  My plan was to covary for sex, icv, 
and age.  I have covaried for icv and age lots of times, but I am 
having trouble covarying (if that is the right word) for this 
categorical sex variable.


Any help would be greatly appreciated!
Jeff

On Wed, Sep 5, 2012 at 10:44 AM, Jeff Sadino > wrote:


Hello,

I am trying to covary for Gender in mri_glmfit, but I am having
errors pop up.  I tried to follow Doug's suggesting in this post:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html
but after modifying my Xg.dat file and rerunning mri_glmfit, it says:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1.53319e+07

I can run it using the --illcond flag, but then I get a bunch of:
***
CEPHES ERROR: fdtrc domain error
***

Can anyone please give advice on how to covary for Gender in
mri_glmfit (or qdec)?

As always, thank you for all of your great help!!
Jeff Sadino




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