Re: [Freesurfer] Basename error

[Douglas N Greve]

If it is not using the basename.m in freesurfer it may fail. Try putting 
$FREESURFER_HOME/fsfast/toolbox first in your matlab path


On 06/22/2014 02:52 PM, Xiaomin Yue wrote:
> Hi Doug
>
> Thanks for you response.  The command line is: selxavg3-sess -s 
> subject_0101 -d . -analysis DoD_looming_lh.
>
> I checked the basename function in the matlab installed in my 
> computer, which is 2010b.  It seems that the basename in the 2010b 
> matlab only accepts one parameter.  I tried two ways to avoid the 
> problem.  First, I replaced the matlab's basename function with my own 
> basename function.  Second, I removed the motion regressor from the 
> analysis.info.  The two method indeed avoided the basename function 
> error, but new errors were created as the following:
>
> Error using ==> fmri_hemodyn
> Too many input argument.
>
> Error in ==> flac_ev2irf at 74
> xirf = fmri_hemodync(tirf, delay, tau, alpha);
>
> Error in ==> flac_desmat at 66
> [xirf tirf] = flac_ev2irf(ev, TER, flac, RefEventDur);
>
> Error in ==> flac_customize at 356
> flacnew = flac_desmat(flacnew);
>
> Error in ==> fast_selxavg3 at 65
> flac0=flac_customize(flac0);
>
>
> I suspected that  the errors was caused by matlab?  if so, what 
> version is required to run 5.3 version correctly?
>
> Thanks for your help!
>
> Xiaomin
>
> 
> Date: Thu, 19 Jun 2014 20:41:28 +0200
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Basename error
>
>
> what is your command line and terminal output
>
>
>
> On 6/19/14 4:36 PM, Xiaomin Yue wrote:
>
> Hi all,
>
> I am analyzing functional data using fsfast 5.3 with the error:
> Error using==> basename.  It seems that the same problem was
> reported before in the mail list
> 
> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021898.html),
> but I can't find answer in the discussion thread in the above link.
>
> Any suggestions?  Thanks,
>
> Xiaomin Yue
>
>
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>
>
>
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> information in this e-mail is intended only for the person to whom it 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] low polygon count like fsaverage3

[Bruce Fischl]

Hi Kai

you mean you want to decimate the surface? You can use 
mris_make_face_parcellation to map something like fsaverage3 to your 
subject.

cheers
Bruce


On Mon, 23 Jun 2014, Kai Schlamp wrote:

> Hello again,
> I am still looking for a way to create a low polygon surface during
> recon-all (where labels still fit). Is there any (expert) option where I can
> specify the number of vertices or distance between vertices? How was
> fsaverage3 (very low polygon count) was created?
> 
> Best regards,
> Kai
> 
>
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Re: [Freesurfer] some questions about optseq

[Douglas N Greve]

I think this is an error I fixed a few months ago. Try this version (for 
linux)
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2


On 06/20/2014 09:05 PM, charujing123 wrote:
> Hi doug, sorry for not enough information sending to you.
> optseq2 --ntp 223 --tr 2 --psdwin 0 20 --ev ev1 2 41 --ev ev2 2 40 
> --nkeep 2 --o ex2 --nsearch 1000 --tnullmin 2 --tnullmax 8
> After running the command above, I get the ex2-001.par and 
> ex2-002.par. In these files, I found that part of NULL window had 10s 
> intervals. However I set the --tnullmax 8, the max time window of NULL 
> should be 8s, not 10s, shouldnot it?
> Also I check the help of optseq2, and it echo "
> Note: it may not be possible for a given parameter set to keep the NULL
> stimulus below a certain amount. In this case, the following error
> message will be printed out 'ERROR: could not enforce tNullMax'. By
> default, tNullMax is infinite."
> But I didnot find any ERROR information in the command window. Is that normal?
> Thanks
> All the best
> Rujing Zha
> 2014-06-21
> 
> charujing123
> 
> *发 件人：*Douglas Greve 
> *发 送时间：*2014-06-20 23:21
> *主 题：*Re: [Freesurfer] some questions about optseq
> *收 件人：*"freesurfer"
> *抄 送：*
>
> weird? I'll need something more specific than that
>
>
> On 6/20/14 4:57 PM, charujing123 wrote:
>> Hi doug
>> Thanks very much. I see. When I add --tnullmin 2 --tnullmax 8, result 
>> looks weird.
>> ===
>> [psylab16@centos1 ~]$ cat ex1-001.par
>> 0. 2 2.000 1. ev2
>> 2. 0 2.000 1. NULL
>> 4. 1 2.000 1. ev1
>> 6. 0 2.000 1. NULL
>> 8. 1 2.000 1. ev1
>> 10. 0 2.000 1. NULL
>> 12. 1 2.000 1. ev1
>> 14. 0 2.000 1. NULL
>> 16. 1 2.000 1. ev1
>> 18. 0 2.000 1. NULL
>> 20. 2 2.000 1. ev2
>> 22. 0 2.000 1. NULL
>> 24. 1 2.000 1. ev1
>> 26. 0 2.000 1. NULL
>> 28. 1 2.000 1. ev1
>> 30. 0 2.000 1. NULL
>> 32. 2 2.000 1. ev2
>> 34. 0 2.000 1. NULL
>> 36. 2 2.000 1. ev2
>> 38. 0 2.000 1. NULL
>> 40. 2 2.000 1. ev2
>> 42. 0 2.000 1. NULL
>> 44. 2 2.000 1. ev2
>> 46. 0 2.000 1. NULL
>> 48. 1 2.000 1. ev1
>> 50. 0 2.000 1. NULL
>> 52. 2 2.000 1. ev2
>> 54. 0 2.000 1. NULL
>> 56. 1 2.000 1. ev1
>> 58. 0 2.000 1. NULL
>> 60. 2 2.000 1. ev2
>> 62. 0 2.000 1. NULL
>> 64. 2 2.000 1. ev2
>> 66. 0 2.000 1. NULL
>> 68. 1 2.000 1. ev1
>> 70. 0 2.000 1. NULL
>> 72. 1 2.000 1. ev1
>> 74. 0 2.000 1. NULL
>> 76. 1 2.000 1. ev1
>> 78. 0 2.000 1. NULL
>> 80. 2 2.000 1. ev2
>> 82. 0 2.000 1. NULL
>> 84. 2 2.000 1. ev2
>> 86. 0 2.000 1. NULL
>> 88. 2 2.000 1. ev2
>> 90. 0 2.000 1. NULL
>> 92. 1 2.000 1. ev1
>> 94. 0 2.000 1. NULL
>> 96. 1 2.000 1. ev1
>> 98. 0 2.000 1. NULL
>> 100. 1 2.000 1. ev1
>> 102. 0 2.000 1. NULL
>> 104. 2 2.000 1. ev2
>> 106. 0 2.000 1. NULL
>> 108. 1 2.000 1. ev1
>> 110. 0 2.000 1. NULL
>> 112. 1 2.000 1. ev1
>> 114. 0 2.000 1. NULL
>> 116. 2 2.000 1. ev2
>> 118. 0 2.000 1. NULL
>> 120. 1 2.000 1. ev1
>> 122. 0 2.000 1. NULL
>> 124. 2 2.000 1. ev2
>> 126. 0 2.000 1. NULL
>> 128. 2 2.000 1. ev2
>> 130. 0 2.000 1. NULL
>> 132. 2 2.000 1. ev2
>> 134. 0 2.000 1. NULL
>> 136. 1 2.000 1. ev1
>> 138. 0 2.000 1. NULL
>> 140. 2 2.000 1. ev2
>> 142. 0 2.000 1. NULL
>> 144. 2 2.000 1. ev2
>> 146. 0 2.000 1. NULL
>> 148. 2 2.000 1. ev2
>> 150. 0 2.000 1. NULL
>> 152. 2 2.000 1. ev2
>> 154. 0 2.000 1. NULL
>> 156. 1 2.000 1. ev1
>> 158. 0 2.000 1. NULL
>> 160. 2 2.000 1. ev2
>> 162. 0 2.000 1. NULL
>> 164. 2 2.000 1. ev2
>> 166. 0 2.000 1. NULL
>> 168. 1 2.000 1. ev1
>> 170. 0 2.000 1. NULL
>> 172. 2 2.000 1. ev2
>> 174. 0 2.000 1. NULL
>> 176. 1 2.000 1. ev1
>> 178. 0 2.000 1. NULL
>> 180. 2 2.000 1. ev2
>> 182. 0 2.000 1. NULL
>> 184. 2 2.000 1. ev2
>> 186. 0 2.000 1. NULL
>> 188. 1 2.000 1. ev1
>> 190. 0 2.000 1. NULL
>> 192. 1 2.000 1. ev1
>> 194. 0 2.000 1. NULL
>> 196. 1 2.000 1. ev1
>> 198. 0 2.000 1. NULL
>> 200. 1 2.000 1. ev1
>> 202. 0 2.000 1. NULL
>> 204. 2 2.000 1. ev2
>> 206. 0 2.000 1. NULL
>> 208. 2 2.000 1. ev2
>> 210. 0 2.000 1. NULL
>> 212. 2 2.000 1. ev2
>> 214. 0 2.000 1. NULL
>

Re: [Freesurfer] Using QDEC for 3 groups x 2 time-points

[Douglas N Greve]

This is a bug in QDEC. I'm surprised it has not surfaced before. It is 
supposed to be looking in "fwhm09" not "fwhm9". One work-around is to 
create a symlink, ie,

cd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/
ln -s fwhm09 fwhm9

otherwise, you will have to run mri_glmfit-sim

doug


On 06/20/2014 11:48 AM, Tudor Popescu wrote:
> Thanks Doug. After using stage#1 of the longitudinal 2-stage model to 
> create cross-sectional measuers of e.g. thickness change from tp1 to 
> tp2 (e.g. thickness-pc1), I then did analyses in QDEC on these 
> measures to see where in the brain such changes are
>
>   * different from zero (within each group); and
>   * different between groups (for every pair of groups in the current
> qdec table, e.g. F vs P)
>
> For thickness-pc1 it all went fine, but for area-pc1 analyses, I get 
> this error right after starting the MonteCarlo Null-Z correction: 
> "Completed loading of analyzed data. fwhm.dat: 8.654965, rounded to 9. 
> ERROR: CSDread(): could not open 
> /usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm9/abs/th13/mc-z.csd".
>  
> This happens regardless of the threshold used (e.g. 0.01 or 0.05)
> In case it's relevant, for the thickness analyses (whose correction 
> worked fine), the fwhm.dat was "10.190419, rounded to 11". I am using 
> FS 5.3.0 (Ubuntu).
>
> Thanks!
> Tudor
>
>
>
> On 17 June 2014 09:29, Douglas Greve  > wrote:
>
>
> It only needs to be accounted for when you compare across all 3
> groups, in which case you'd have to use mri_glmfit
> doug
>
>
>
> On 6/17/14 12:07 AM, Tudor Popescu wrote:
>> Hi Doug,
>>
>> Thanks... Presumably I'd just leave each possible pair of groups
>> at a time in the qdec table, and delete rows corresponding to
>> subjects of the remaining group? And then do stats on, e.g.
>> "long.thickness-rate" to compare rate of change between the
>> current pair of groups?
>> Doesn't variability across all 3 groups somehow have to be
>> accounted for?
>>
>> Tudor
>>
>>
>> On 16 June 2014 20:38, Douglas Greve > > wrote:
>>
>>
>> Yes, you could do each separately.
>> doug
>>
>>
>>
>> On 6/16/14 8:10 PM, Tudor Popescu wrote:
>>> Dear FS list,
>>>
>>> I have a data set with 3 groups (2 treatments, 1 control),
>>> each with equally-spaced time-points (pre and post
>>> structural scan). I've done the 3 longitudinal
>>> pre-processing steps, and stage#1 of the two-stage model,
>>> and I would prefer to run stage#2 (cross-sectional analysis
>>> of the difference) with QDEC as opposed to with mri_glmfit.
>>>
>>> I know that QDEC is meant for 2 groups, but I see that
>>> designs with 4 or 6 groups can be analysed with QDEC (as per
>>> this
>>> 
>>> FSGD examples page) whereas designs with 3 groups cannot be.
>>> It seems to me that an even number of groups is QDEC-able
>>> while an odd number isn't, but is there any workaround so
>>> that I can still use QDEC? Perhaps if I only do pairwise
>>> comparisons one at a time, i.e. treatment1 vs control and
>>> treatment2 vs control?
>>>
>>> Many thanks!
>>> Tudor
>>>
>>>
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>>> 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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>>
>>
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> The informati

Re: [Freesurfer] Retinotopic mapping using selxavg3-sess

[Douglas N Greve]

Do you have FSL installed? If so, what is your $FSLDIR?


On 06/19/2014 03:03 PM, Alan Lee wrote:
>
> Thanks, Doug. I think I've kind of sorted that one out by creating a 
> folder called "Retinotopy" under 
> freesurfer/subjects/Retinotopy/3/, which contains the 001/, ... 
> 004/ folders containing those their corresponding (polar and eccen) 
> rtopy.par and f.nii files.
>
> But now I have another problem. When I run
>
> selxavg3-sess -a Retintopy.3.lh -s 3
>
> , it runs up to the point as below, where it's "using FSL's BET to 
> Extract Brain".
>
> # -- Using FSL's BET to Extract Brain-- #
> /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy
> bet.fsl /tmp/mkbrainmask_9112/in.nii /tmp/mkbrainmask_9112/brain -m -f 0.1
> /usr/local/freesurfer//bin/bet.fsl: 1: 
> /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found
> /usr/local/freesurfer//bin/bet.fsl: 1: 
> /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found
> /usr/local/freesurfer//bin/bet.fsl: 1: 
> /usr/local/freesurfer//bin/bet.fsl: /bin/imtest: not found
> /usr/local/freesurfer//bin/bet.fsl: 153: [: =: unexpected operator
> /usr/local/freesurfer//bin/bet.fsl: 231: 
> /usr/local/freesurfer//bin/bet.fsl: /bin/bet2: not found
>
> Then I realized that the program looks for those not-found 
> files (remove_ext, imtest, bet2) in /bin/, but actually they're all in 
> /usr/lib/fsl/5.0/.
>
> What I did next was to copy those files from /usr/lib/fsl/5.0/ to 
> /bin/, but then I got this error:
>
> # -- Using FSL's BET to Extract Brain-- #
> /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy
> bet.fsl /tmp/mkbrainmask_12619/in.nii /tmp/mkbrainmask_12619/brain -m 
> -f 0.1
> /bin/bet2: error while loading shared libraries: libfslvtkio.so: 
> cannot open shared object file: No such file or directory
> mri_binarize --i /tmp/mkbrainmask_12619/brain_mask.nii --min .01 --o 
> /tmp/mkbrainmask_12619/brain_mask.nii
> niiRead(): error opening file /tmp/mkbrainmask_12619/brain_mask.nii
>
> Again, I tried copying the file libfslvtkio.so from /usr/lib/fsl/5.0 
> to /bin/, but it keeps giving me the same error.
>
> So I have two questions:
> 1) I suspect that selxavg3-sess should be looking for the files in 
> /usr/lib/fsl/5.0 instead of in /bin/. Why does it do that? And how can 
> I direct it to look for files in the former location instead?
> 2) As a quick fix, is it OK for me to copy all the files from 
> /usr/lib/fsl/5.0 to /bin/? Will it solve the problem? The folder /bin/ 
> contains something else and I don't really feel like messing with it.
>
> Many thanks,
> Alan
>
>
>
>
>
> --
> Alan Lee
> sites.google.com/site/alanlflee/ 
>
>
> On Tue, Jun 17, 2014 at 4:54 PM, Douglas Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> It looks for it in the current folder. You must run this from the
> same folder you ran mkanalysis-sess from (which should be your
> project folder)
>
>
>
>
> On 6/17/14 4:13 PM, Alan Lee wrote:
>> Hello,
>>
>> I'm using freesurfer to do retinotopic mapping. I've completed
>> the recon-all, mkanalysis-sess, mri-convert and preproc-sess
>> steps. Now when I run the selxavg3-sess (my subject name is 3):
>>
>> selxavg3-sess -a Retinotopy.3.lh -s 3
>>
>> I got the following message:
>> "ERROR:
>> /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy does
>> not exist"
>>
>> It seems to look for a Retintopy folder within
>> /Retinotopy/3/. I suppose the Retinotopy folder should be
>> placed under freesurfer/subjects/ ? Am I missing something here?
>>
>> Any help would be greatly appreciated.
>>
>> Many thanks,
>> Alan
>>
>> =
>> debian:/usr/local/freesurfer/subjects/Retinotopy# selxavg3-sess
>> -a Retinotopy.3.lh -s 3
>> Surface data self lh
>> --
>> selxavg3-sess logfile is
>> 
>> /usr/local/freesurfer/subjects/Retinotopy/log/selxavg3-sess-Retinotopy-Retinotopy.3.lh-140617154401.log
>> --
>> preproc-sess -s 3 -d
>> /usr/local/freesurfer/subjects/Retinotopy -a Retinotopy.3.lh
>> -nolog
>> --
>> preproc-sess logfile is /dev/null
>> --
>> $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
>> root
>> setenv FREESURFER_HOME /usr/local/freesurfer/
>> setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/Structural
>> Linux debian 3.2.0-4-486 #1 Debian 3.2.57-3+deb7u1 i686 GNU/Linux
>> /usr/local/freesurfer/subjects/Retinotopy
>> /usr/local/freesurfer//fsfast/bin/preproc-sess
>> -s 3 -d /usr/local/freesurfer/subjects/Retinotopy -a
>> Retinotopy.3

Re: [Freesurfer] Group analysis over different studies?

[Douglas N Greve]

Sorry, yes, I meant ces instead of gamma. It is not set up to use CVS. 
On my todo list...

On 06/17/2014 03:13 PM, Terri Scott wrote:
> Hi Doug,
>
> Is gamma.mgh the same as ces.nii.gz? I'm working with data processed 
> with an older version of Freesurfer, not exactly sure which. I have a 
> related question also; the masks and meanfunc images don't seem to be 
> lining up that well after running isxconcat-sess. Would is be possible 
> for me to use cvs normalization on these data before concatenating 
> within each study? I have run the cvs transformations already, but I'm 
> not sure how I would chose which functional data to apply them to, and 
> if I'd need to set up a new filesystem for the normalized data.
>
> Thanks again!
> Terri
>
>
> On Tue, Jun 17, 2014 at 4:27 AM, Douglas Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> Just run isxconcat-sess for each study, then
>
> mri_concat study1/gamma.mgh study2/gamma.mgh --o
> study1-and-study2-gamma.mgh
>
> then run mri_glmfit on the above output
>
> doug
>
>
>
> On 6/16/14 11:54 PM, Terri Scott wrote:
>> Hi all,
>>
>> I want to do a group analysis using subjects that were run in
>> different studies but who have (some of) the same relevant
>> functional contrasts. Is there a way to run something like
>> isxconcat-sess on data from different analysis streams? Or if
>> not, which files do I need to collect and align from each subject
>> in order to run mri_glmfit? What would be the best way to handle
>> this analysis?
>>
>> Thanks,
>> Terri
>>
>>
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>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Project probabilistic connectivity maps to pial and calculate mass center

[Douglas N Greve]

I'm not sure all that you are trying to do, but if you have a 
registration that maps to the orig.mgz, then you can use mri_vol2surf to 
map to the pial surface. Run it with --help to get more info
doug


On 06/20/2014 12:26 AM, gong jinnan wrote:
> Dear all,
> I have used probabilistic tractography methods by FSL-FDT to get 
> probabilistic connectivity between grey-white matter interface of 
> precentral and basal ganglia in subjects’ space. The latter one was 
> used as classification mask. And then all of tractography maps were 
> registered to MNI space.
> Now I want to project tractography results like seed_to_BG.nii.gz to 
> pial in Freesurfer and calculate mass center of those maps. But 
> unfortunately I am not clear how to do that. So there is my question:
> 1.It is not difficult to project seed_to_BG.nii.gz to 
> .../mri/orig.mgz. But how to project to pial after that?
> 2.How can I get mass center like pictures in attachment. I tried 
> calculated mass center of seed_to_BG.nii.gz in MNI space, but the mass 
> center point does not fall in precentral. So I want to do that in pial.
> 3.How to transform subjects’ pial to talairach pial?
> I searched method to do that for a long time, but have no idea yet. So 
> I hope I can get valuable suggestions here.
> I will be grateful if you can help me!
>
> Sincerely，
> Jinnan Gong
> Best wishes for you!
> Key Laboratory for NeuroInformation of Ministry of Education, School 
> of Life Science and Technology, University of Electronic Science and 
> Technology of China
>
>
>
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Re: [Freesurfer] Labels to annotation

[Douglas N Greve]

Don't use FreeSurferColorLUT.txt, you need to create your own color 
table whose format is like FreeSurferColorLUT.txt
doug

On 06/20/2014 03:49 AM, Karen Marie Sandø Ambrosen wrote:
> Hi Bruce,
>
> When I input all the labels in the mris_label2annot command I get the 
> result shown in: H09_copy_AllLabels2annot.png and it gives a lot of 
> warnings: "Warning: vertex 142382 with annotation  - out of 
> range!".
> The command I use looks like:
> mris_label2annot --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --l 
> label1 --l label2 ... --labeln --s H09_copy --a output_annotation --h lh
> When I run the command I get a lot of warnings: "WARNING: vertex 
> 139930 maps to multiple labels! (overwriting)".
>
> In comparison if I create an annotation using only, e.g., the first 10 
> labels I get the result shown in: H09_copy_10Labels2annot.png and I 
> don't get any warnings.
> If I create an annotation using the first 100 labels I get the result 
> shown in: H09_copy_100Labels2annot.png and I get warnings similar to 
> when I use all the labels.
>
> I hope this makes the problem more clear.
>
> Best,
> Karen
>
>
> On 06/20/2014 04:02 AM, Bruce Fischl wrote:
>> Hi Karen
>> What do you mean the results don't look right? Can you send an image?
>> Cheers
>> Bruce
>>
>>> On Jun 19, 2014, at 9:41 AM, Karen Marie Sandø Ambrosen 
>>>  wrote:
>>>
>>> Dear Freesurfer experts,
>>>
>>> I have made a parcellation of the white matter surface outside of
>>> freesurfer in volumes. I convert the volume labels to surface labels. I
>>> have now a lot of surface labels (~500 for each hemisphere) which I 
>>> want
>>> to concatenate to an annotation file for easier visualization. When I
>>> use mris_label2annot to perform this operation I get a lot of warnings:
>>> "WARNING: vertex 6021 maps to multiple labels! (overwriting)", and the
>>> result does not look right. When I load some of the single labels into
>>> freeview or tksurfer they look fine. Does anyone know how to perform
>>> this operation? How do I avoid the warnings?
>>>
>>> I do the operations (volume labels-->surface labels-->annotation) on
>>> each hemisphere separately, but I have some regions located in both
>>> hemispheres. Is it then possible to keep the whole region the same 
>>> color
>>> across hemispheres during the operations?
>>>
>>> Best,
>>> Karen
>>> ___
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>>>
>>>
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>>
>>
>> The information in this e-mail is intended only for the person to 
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and 
>> the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to 
>> you in error
>> but does not contain patient information, please contact the sender 
>> and properly
>> dispose of the e-mail.
>
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] How to extract significant result for each subject

[Douglas N Greve]

If you run mri_glmfit-sim, it will extract this for you. Run it with 
--help to get more information
doug

On 06/12/2014 10:53 PM, kangchengwang0...@gmail.com wrote:
> Dear freesurfers,
>I contrast depression and control and find that patients have a 
> lower thickness in region of inferior frontal gyrus. Now, I want to 
> extract the data of thickness for each subject. Could you tell which 
> command could do this?
> Thank you
> 
>
> Wang Kangcheng ( New learner of freesurfer )
>
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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[Freesurfer] surface to volume visualization

[james pardon]

Dear all,

I'm looking for a way to automate surface on volume visualization, to check
if the surface reconstruction have been successful on a very large number
of subjects. Normally, I would use freeview with -f and -v flags to check
and see if it is necessary to edit controls points, etc.

As an example, one option to automate this process is to use freeview
snapshot option and write a script that runs on several hundred subjects
and then show all the resulting images in html format.  Running freeview
with snapshot option works really good, however, since every freeview run
needs X11 there is an overhead here, especially when I'm running on a
remote cluster with no X11, which makes running X11 almost impossible.

I'm wondering whether any one has a better idea for this?

Thanks
James
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Re: [Freesurfer] Vertex analysis cluster values

[Douglas N Greve]

Hi Rachel, are you saying that there does not seem to be an effect in 
the mean using the same contrast that was used to compute the clusters? 
How are you doing the test in the mean? Are you sure you have the same 
design and contrast matrices?

doug


On 06/06/2014 02:38 PM, Rachel Jonas wrote:
> Hi Freesurfer users,
>
> I ran a GLM vertex analysis testing an interaction between group and a 
> task measure, and a few clusters popped up that survived correction. I 
> extracted the mean thickness values at the clusters (using 
> cache.th13.abs.y.ocn.dat) in order to plot these interactions in graph 
> form. When I did this, the interactions look nonexistent, and there 
> doesn't appear to be any relationships between my task measure and 
> thickness in either group.
>
> My FSGD file contains 4 groups (patients & controls with two different 
> scanner sites), and my continuous variables are age and this task 
> measure. I only have 15 patients and 15 controls, so my only thought 
> so far is that my power is low, and these results are spurious.
>
> My contrast file is:
> 0 0 0 0 0 0 0 0 0.5 0.5 -0.5  -0.5
>
> Any insight would be greatly appreciated! Thank you!
>
> Rachel
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Basename error

[Xiaomin Yue]

Hi Doug,
Thanks very much for the information.  I will try it.
XIaomin
> Date: Mon, 23 Jun 2014 09:19:20 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Basename error
> 
> If it is not using the basename.m in freesurfer it may fail. Try putting 
> $FREESURFER_HOME/fsfast/toolbox first in your matlab path
> 
> 
> On 06/22/2014 02:52 PM, Xiaomin Yue wrote:
> > Hi Doug
> >
> > Thanks for you response.  The command line is: selxavg3-sess -s 
> > subject_0101 -d . -analysis DoD_looming_lh.
> >
> > I checked the basename function in the matlab installed in my 
> > computer, which is 2010b.  It seems that the basename in the 2010b 
> > matlab only accepts one parameter.  I tried two ways to avoid the 
> > problem.  First, I replaced the matlab's basename function with my own 
> > basename function.  Second, I removed the motion regressor from the 
> > analysis.info.  The two method indeed avoided the basename function 
> > error, but new errors were created as the following:
> >
> > Error using ==> fmri_hemodyn
> > Too many input argument.
> >
> > Error in ==> flac_ev2irf at 74
> > xirf = fmri_hemodync(tirf, delay, tau, alpha);
> >
> > Error in ==> flac_desmat at 66
> > [xirf tirf] = flac_ev2irf(ev, TER, flac, RefEventDur);
> >
> > Error in ==> flac_customize at 356
> > flacnew = flac_desmat(flacnew);
> >
> > Error in ==> fast_selxavg3 at 65
> > flac0=flac_customize(flac0);
> >
> >
> > I suspected that  the errors was caused by matlab?  if so, what 
> > version is required to run 5.3 version correctly?
> >
> > Thanks for your help!
> >
> > Xiaomin
> >
> > 
> > Date: Thu, 19 Jun 2014 20:41:28 +0200
> > From: gr...@nmr.mgh.harvard.edu
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Basename error
> >
> >
> > what is your command line and terminal output
> >
> >
> >
> > On 6/19/14 4:36 PM, Xiaomin Yue wrote:
> >
> > Hi all,
> >
> > I am analyzing functional data using fsfast 5.3 with the error:
> > Error using==> basename.  It seems that the same problem was
> > reported before in the mail list
> > 
> > (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021898.html),
> > but I can't find answer in the discussion thread in the above link.
> >
> > Any suggestions?  Thanks,
> >
> > Xiaomin Yue
> >
> >
> > ___
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> > 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.
> >
> >
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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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> 
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[Freesurfer] Edits, where art thou?

[Max Svensson]

Hi! When I edit my data, for instance wm editing, I do not see the changes
applied to the original image. To make you understand what I do:

Open up freeview, load the image, Wm and brainmask, with wm at the top.
Then I go into voxel edit, press recon edit, and start filling in
topographical defects and do some wm editing. HOWEVER, after I run recon
all (recon-all -autorecon2 -autorecon3 -subjid anon)and it's finished
without problems, I do not see the edits done on my image. Sure, I see the
yellow colour which I filled some spots with, but I was thinking that I
would see an edited image, that is with pia (topographical defects) and wm
surface going out to the areas I edited. Not only yellow filling which was
there before since I edited. Am I doing something wrong? Is the
reconprocessed images hidden out there somewhere?
Freesurfer team, please help!

Best,
MAX
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[Freesurfer] recon-all ERROR, no idea why

[Remy Wahnoun]

hello, freesurfers,
Im having trouble using recon-all, I tried the prebuilt virtual machine and
a fresh unbuntu install without luck.
Would anyone have a look at my recon-all.log? I cant spot any error.
*Thanks *

*Rémy Wahnoun, PhD*
Biomedical Research Group Manager
Barrow Neurological Institute at Phoenix Children's Hospital
Adjunct Faculty, Arizona State University
*www.NeuralControl.net *






Mon Jun 23 11:35:42 EDT 2014
/media/sf_Imagery/FreeSurfer/xx
/usr/local/freesurfer/bin/recon-all
-i
/media/sf_Imagery/Sorted/xx/xx_S601_MRI_BRAIN_WO_CONTRAST_TRANSVERSAL(110)/ser601img1.dcm
-subjid xx -sd /media/sf_Imagery/FreeSurfer -all
subjid xx
setenv SUBJECTS_DIR /media/sf_Imagery/FreeSurfer
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0
Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48
UTC 2014 i686 i686 i386 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 64 kbytes
maxproc  28136
maxlocks unlimited
maxsignal28136
maxmessage   819200
maxnice  0
maxrtprio0
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:   3616064 6924002923664  0  94528 405020
-/+ buffers/cache: 1928523423212
Swap:  1944572  01944572


program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion:
$Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT  BuildTimeStamp: May
13 2013 18:53:32  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
mreuter Exp $  User: fsuser  Machine: xubuntu-VirtualBox  Platform: Linux
 PlatformVersion: 3.2.0-64-generic  CompilerName: GCC  CompilerVersion:
30400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info
 ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT
 BuildTimeStamp: May 13 2013 18:53:32  CVS: $Id: tkregister2.c,v 1.121.2.1
2011/03/28 20:25:16 greve Exp $  User: fsuser  Machine: xubuntu-VirtualBox
 Platform: Linux  PlatformVersion: 3.2.0-64-generic  CompilerName: GCC
 CompilerVersion: 30400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu)
on 2010-02-20 at 20:19:13
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion:
$Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT  BuildTimeStamp: May
13 2013 18:53:32  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14
nicks Exp $  User: fsuser  Machine: xubuntu-VirtualBox  Platform: Linux
 PlatformVersion: 3.2.0-64-generic  CompilerName: GCC  CompilerVersion:
30400
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion:
$Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT  BuildTimeStamp: May
13 2013 18:53:32  CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32
nicks Exp $  User: fsuser  Machine: xubuntu-VirtualBox  Platform: Linux
 PlatformVersion: 3.2.0-64-generic  CompilerName: GCC  CompilerVersion:
30400
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion:
$Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT  BuildTimeStamp: May
13 2013 18:53:32  CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08
22:18:44 nicks Exp $  User: fsuser  Machine: xubuntu-VirtualBox  Platform:
Linux  PlatformVersion: 3.2.0-64-generic  CompilerName: GCC
 CompilerVersion: 30400
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name:
stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT  BuildTimeStamp: May 13 2013
18:53:32  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $
 User: fsuser  Machine: xubuntu-VirtualBox  Platform: Linux
 PlatformVersion: 3.2.0-64-generic  CompilerName: GCC  CompilerVersion:
30400
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion:
$Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT  BuildTimeStamp: May
13 2013 18:53:32  CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks
Exp $  User: fsuser  Machine: xubuntu-VirtualBox  Platform: Linux
 PlatformVersion: 3.2.0-64-generic  CompilerName: GCC  CompilerVersion:
30400
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion:
$Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT  BuildTimeStamp: May
13 2013 18:53:32  CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02
16:26:15 greve Exp $  User: fsuser  Machine: xubuntu-VirtualBox  Platform:
Linux  PlatformVersion: 3.2.0-64-generic  CompilerName: GCC
 CompilerVersion: 30400
ProgramName: mri_em_register  Pr

Re: [Freesurfer] Why the result was not same for the same subject

[Nick Schmansky, MGH]

Wang,

what command-line flags were included?  can you send me the recon-all.log file 
for these runs?  The results should be the same with repeated runs if the 
default flags were used.

Nick


On Jun 21, 2014, at 10:20 PM, wangkangcheng_gmail  
wrote:

> Dear Bruce
> 
>   Yes. The following is an example result for the subject (The id from Sub_1 
> to Sub_10 is the same subject) that I calculate ten times. 
> 
> 
> rh.aparc.a2009s.volume rh_G_and_S_frontomargin_volume
> Sub_1 1713
> Sub_2 1950
> Sub_3 1789
> Sub_4 1783
> Sub_5 1879
> Sub_6 1778
> Sub_7 1892
> Sub_8 1782
> Sub_9 1799
> Sub_101799
> 
> 
> Thank you 
> 
> Wang Kangcheng
> 
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Re: [Freesurfer] recon-all ERROR, no idea why

[Douglas N Greve]

can you run the command below and send nu.log?

cd /media/sf_Imagery/FreeSurfer/xx/mri

mri_nu_correct.mni --debug --n 1 --proto-iters 1000 --distance 50 
--no-rescale --i orig.mgz --o orig_nu.mgz  |& tee nu.log




On 06/23/2014 11:49 AM, Remy Wahnoun wrote:
> hello, freesurfers,
> Im having trouble using recon-all, I tried the prebuilt virtual 
> machine and a fresh unbuntu install without luck.
> Would anyone have a look at my recon-all.log? I cant spot any error.
> /Thanks /
> /
> /
> *Rémy Wahnoun, PhD*
> Biomedical Research Group Manager
> Barrow Neurological Institute at Phoenix Children's Hospital
> Adjunct Faculty, Arizona State University
> /www.NeuralControl.net /
>
>
>
>
>
>
> Mon Jun 23 11:35:42 EDT 2014
> /media/sf_Imagery/FreeSurfer/xx
> /usr/local/freesurfer/bin/recon-all
> -i 
> /media/sf_Imagery/Sorted/xx/xx_S601_MRI_BRAIN_WO_CONTRAST_TRANSVERSAL(110)/ser601img1.dcm
>  
> -subjid xx -sd /media/sf_Imagery/FreeSurfer -all
> subjid xx
> setenv SUBJECTS_DIR /media/sf_Imagery/FreeSurfer
> FREESURFER_HOME /usr/local/freesurfer
> Actual FREESURFER_HOME /usr/local/freesurfer
> build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0
> Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 
> 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux
> cputime  unlimited
> filesize unlimited
> datasize unlimited
> stacksize8192 kbytes
> coredumpsize 0 kbytes
> memoryuseunlimited
> vmemoryuse   unlimited
> descriptors  1024
> memorylocked 64 kbytes
> maxproc  28136
> maxlocks unlimited
> maxsignal28136
> maxmessage   819200
> maxnice  0
> maxrtprio0
> maxrttimeunlimited
>
>  total   used   free shared  buffers cached
> Mem:   3616064 6924002923664  094528 405020
> -/+ buffers/cache: 1928523423212
> Swap:  1944572  01944572
>
> 
> program versions used
> $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
> $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
> mri_convert -all-info
> ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: 
> $Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT  BuildTimeStamp: 
> May 13 2013 18:53:32  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 
> 21:55:16 mreuter Exp $  User: fsuser  Machine: xubuntu-VirtualBox 
>  Platform: Linux  PlatformVersion: 3.2.0-64-generic  CompilerName: GCC 
>  CompilerVersion: 30400
> FLIRT version 5.5
> $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
> mri_convert --version
> stable5
> ProgramName: tkregister2_cmdl  ProgramArguments: --all-info 
>  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT 
>  BuildTimeStamp: May 13 2013 18:53:32  CVS: $Id: tkregister2.c,v 
> 1.121.2.1 2011/03/28 20:25:16 greve Exp $  User: fsuser  Machine: 
> xubuntu-VirtualBox  Platform: Linux  PlatformVersion: 3.2.0-64-generic 
>  CompilerName: GCC  CompilerVersion: 30400
> Program nu_correct, built from:
> Package MNI N3, version 1.10, compiled by nicks@fishie 
> (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13
> ProgramName: mri_make_uchar  ProgramArguments: -all-info 
>  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT 
>  BuildTimeStamp: May 13 2013 18:53:32  CVS: $Id: mri_make_uchar.c,v 
> 1.4 2011/03/02 00:04:14 nicks Exp $  User: fsuser  Machine: 
> xubuntu-VirtualBox  Platform: Linux  PlatformVersion: 3.2.0-64-generic 
>  CompilerName: GCC  CompilerVersion: 30400
> ProgramName: mri_normalize  ProgramArguments: -all-info 
>  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT 
>  BuildTimeStamp: May 13 2013 18:53:32  CVS: $Id: mri_normalize.c,v 
> 1.73.2.1 2012/10/17 19:11:32 nicks Exp $  User: fsuser  Machine: 
> xubuntu-VirtualBox  Platform: Linux  PlatformVersion: 3.2.0-64-generic 
>  CompilerName: GCC  CompilerVersion: 30400
> ProgramName: mri_watershed  ProgramArguments: -all-info 
>  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT 
>  BuildTimeStamp: May 13 2013 18:53:32  CVS: $Id: mri_watershed.cpp,v 
> 1.96.2.1 2011/11/08 22:18:44 nicks Exp $  User: fsuser  Machine: 
> xubuntu-VirtualBox  Platform: Linux  PlatformVersion: 3.2.0-64-generic 
>  CompilerName: GCC  CompilerVersion: 30400
> ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: 
> $Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT  BuildTimeStamp: 
> May 13 2013 18:53:32  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 
> 00:04:16 nicks Exp $  User: fsuser  Machine: xubuntu-VirtualBox 
>  Platform: Linux  PlatformVersion: 3.2.0-64-generic  CompilerName: GCC 
>  CompilerVersion: 30400
> ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: 
> $Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT  BuildTimeStamp: 
> May 13 2013 18:53:32  CVS: $Id: mri_segment.c,v 1.40 2011/03/02 
> 00:04:24 nicks Exp $  User: fsuser  Machine: xubuntu-VirtualBox 

Re: [Freesurfer] Retinotopic mapping using selxavg3-sess

[Alan Lee]

Yes, I've installed FSL already. I can launch FSL by typing "fslview" in
the command window.

However, it seems that the $FSLDIR is not defined. Should I define it
manually using setenv before running selxavg3-sess?





--
Alan Lee
sites.google.com/site/alanlflee/


On Mon, Jun 23, 2014 at 4:03 PM, Douglas N Greve 
wrote:

>
> Do you have FSL installed? If so, what is your $FSLDIR?
>
>
> On 06/19/2014 03:03 PM, Alan Lee wrote:
> >
> > Thanks, Doug. I think I've kind of sorted that one out by creating a
> > folder called "Retinotopy" under
> > freesurfer/subjects/Retinotopy/3/, which contains the 001/, ...
> > 004/ folders containing those their corresponding (polar and eccen)
> > rtopy.par and f.nii files.
> >
> > But now I have another problem. When I run
> >
> > selxavg3-sess -a Retintopy.3.lh -s 3
> >
> > , it runs up to the point as below, where it's "using FSL's BET to
> > Extract Brain".
> >
> > # -- Using FSL's BET to Extract Brain-- #
> > /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy
> > bet.fsl /tmp/mkbrainmask_9112/in.nii /tmp/mkbrainmask_9112/brain -m -f
> 0.1
> > /usr/local/freesurfer//bin/bet.fsl: 1:
> > /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found
> > /usr/local/freesurfer//bin/bet.fsl: 1:
> > /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found
> > /usr/local/freesurfer//bin/bet.fsl: 1:
> > /usr/local/freesurfer//bin/bet.fsl: /bin/imtest: not found
> > /usr/local/freesurfer//bin/bet.fsl: 153: [: =: unexpected operator
> > /usr/local/freesurfer//bin/bet.fsl: 231:
> > /usr/local/freesurfer//bin/bet.fsl: /bin/bet2: not found
> >
> > Then I realized that the program looks for those not-found
> > files (remove_ext, imtest, bet2) in /bin/, but actually they're all in
> > /usr/lib/fsl/5.0/.
> >
> > What I did next was to copy those files from /usr/lib/fsl/5.0/ to
> > /bin/, but then I got this error:
> >
> > # -- Using FSL's BET to Extract Brain-- #
> > /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy
> > bet.fsl /tmp/mkbrainmask_12619/in.nii /tmp/mkbrainmask_12619/brain -m
> > -f 0.1
> > /bin/bet2: error while loading shared libraries: libfslvtkio.so:
> > cannot open shared object file: No such file or directory
> > mri_binarize --i /tmp/mkbrainmask_12619/brain_mask.nii --min .01 --o
> > /tmp/mkbrainmask_12619/brain_mask.nii
> > niiRead(): error opening file /tmp/mkbrainmask_12619/brain_mask.nii
> >
> > Again, I tried copying the file libfslvtkio.so from /usr/lib/fsl/5.0
> > to /bin/, but it keeps giving me the same error.
> >
> > So I have two questions:
> > 1) I suspect that selxavg3-sess should be looking for the files in
> > /usr/lib/fsl/5.0 instead of in /bin/. Why does it do that? And how can
> > I direct it to look for files in the former location instead?
> > 2) As a quick fix, is it OK for me to copy all the files from
> > /usr/lib/fsl/5.0 to /bin/? Will it solve the problem? The folder /bin/
> > contains something else and I don't really feel like messing with it.
> >
> > Many thanks,
> > Alan
> >
> >
> >
> >
> >
> > --
> > Alan Lee
> > sites.google.com/site/alanlflee/ <
> http://sites.google.com/site/alanlflee/>
> >
> >
> > On Tue, Jun 17, 2014 at 4:54 PM, Douglas Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > It looks for it in the current folder. You must run this from the
> > same folder you ran mkanalysis-sess from (which should be your
> > project folder)
> >
> >
> >
> >
> > On 6/17/14 4:13 PM, Alan Lee wrote:
> >> Hello,
> >>
> >> I'm using freesurfer to do retinotopic mapping. I've completed
> >> the recon-all, mkanalysis-sess, mri-convert and preproc-sess
> >> steps. Now when I run the selxavg3-sess (my subject name is 3):
> >>
> >> selxavg3-sess -a Retinotopy.3.lh -s 3
> >>
> >> I got the following message:
> >> "ERROR:
> >> /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy does
> >> not exist"
> >>
> >> It seems to look for a Retintopy folder within
> >> /Retinotopy/3/. I suppose the Retinotopy folder should be
> >> placed under freesurfer/subjects/ ? Am I missing something here?
> >>
> >> Any help would be greatly appreciated.
> >>
> >> Many thanks,
> >> Alan
> >>
> >> =
> >> debian:/usr/local/freesurfer/subjects/Retinotopy# selxavg3-sess
> >> -a Retinotopy.3.lh -s 3
> >> Surface data self lh
> >> --
> >> selxavg3-sess logfile is
> >>
> /usr/local/freesurfer/subjects/Retinotopy/log/selxavg3-sess-Retinotopy-Retinotopy.3.lh-140617154401.log
> >> --
> >> preproc-sess -s 3 -d
> >> /usr/local/freesurfer/subjects/Retinotopy -a Retinotopy.3.lh
> >> -nolog
> >> --
> >> preproc-sess logfile is /d

Re: [Freesurfer] Retinotopic mapping using selxavg3-sess

[Douglas N Greve]

Yes. I'm surprised that FSL would run at all without that defined.
doug

On 06/23/2014 12:44 PM, Alan Lee wrote:
> Yes, I've installed FSL already. I can launch FSL by typing "fslview" 
> in the command window.
>
> However, it seems that the $FSLDIR is not defined. Should I define it 
> manually using setenv before running selxavg3-sess?
>
>
>
>
>
> --
> Alan Lee
> sites.google.com/site/alanlflee/ 
>
>
> On Mon, Jun 23, 2014 at 4:03 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> Do you have FSL installed? If so, what is your $FSLDIR?
>
>
> On 06/19/2014 03:03 PM, Alan Lee wrote:
> >
> > Thanks, Doug. I think I've kind of sorted that one out by creating a
> > folder called "Retinotopy" under
> > freesurfer/subjects/Retinotopy/3/, which contains the 001/, ...
> > 004/ folders containing those their corresponding (polar and eccen)
> > rtopy.par and f.nii files.
> >
> > But now I have another problem. When I run
> >
> > selxavg3-sess -a Retintopy.3.lh -s 3
> >
> > , it runs up to the point as below, where it's "using FSL's BET to
> > Extract Brain".
> >
> > # -- Using FSL's BET to Extract Brain-- #
> > /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy
> > bet.fsl /tmp/mkbrainmask_9112/in.nii /tmp/mkbrainmask_9112/brain
> -m -f 0.1
> > /usr/local/freesurfer//bin/bet.fsl: 1:
> > /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found
> > /usr/local/freesurfer//bin/bet.fsl: 1:
> > /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found
> > /usr/local/freesurfer//bin/bet.fsl: 1:
> > /usr/local/freesurfer//bin/bet.fsl: /bin/imtest: not found
> > /usr/local/freesurfer//bin/bet.fsl: 153: [: =: unexpected operator
> > /usr/local/freesurfer//bin/bet.fsl: 231:
> > /usr/local/freesurfer//bin/bet.fsl: /bin/bet2: not found
> >
> > Then I realized that the program looks for those not-found
> > files (remove_ext, imtest, bet2) in /bin/, but actually they're
> all in
> > /usr/lib/fsl/5.0/.
> >
> > What I did next was to copy those files from /usr/lib/fsl/5.0/ to
> > /bin/, but then I got this error:
> >
> > # -- Using FSL's BET to Extract Brain-- #
> > /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy
> > bet.fsl /tmp/mkbrainmask_12619/in.nii
> /tmp/mkbrainmask_12619/brain -m
> > -f 0.1
> > /bin/bet2: error while loading shared libraries: libfslvtkio.so:
> > cannot open shared object file: No such file or directory
> > mri_binarize --i /tmp/mkbrainmask_12619/brain_mask.nii --min .01 --o
> > /tmp/mkbrainmask_12619/brain_mask.nii
> > niiRead(): error opening file /tmp/mkbrainmask_12619/brain_mask.nii
> >
> > Again, I tried copying the file libfslvtkio.so from /usr/lib/fsl/5.0
> > to /bin/, but it keeps giving me the same error.
> >
> > So I have two questions:
> > 1) I suspect that selxavg3-sess should be looking for the files in
> > /usr/lib/fsl/5.0 instead of in /bin/. Why does it do that? And
> how can
> > I direct it to look for files in the former location instead?
> > 2) As a quick fix, is it OK for me to copy all the files from
> > /usr/lib/fsl/5.0 to /bin/? Will it solve the problem? The folder
> /bin/
> > contains something else and I don't really feel like messing
> with it.
> >
> > Many thanks,
> > Alan
> >
> >
> >
> >
> >
> > --
> > Alan Lee
> > sites.google.com/site/alanlflee/
> 
> 
> >
> >
> > On Tue, Jun 17, 2014 at 4:54 PM, Douglas Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
> >
> >
> > It looks for it in the current folder. You must run this
> from the
> > same folder you ran mkanalysis-sess from (which should be your
> > project folder)
> >
> >
> >
> >
> > On 6/17/14 4:13 PM, Alan Lee wrote:
> >> Hello,
> >>
> >> I'm using freesurfer to do retinotopic mapping. I've completed
> >> the recon-all, mkanalysis-sess, mri-convert and preproc-sess
> >> steps. Now when I run the selxavg3-sess (my subject name is
> 3):
> >>
> >> selxavg3-sess -a Retinotopy.3.lh -s 3
> >>
> >> I got the following message:
> >> "ERROR:
> >> /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy does
> >> not exist"
> >>
> >> It seems to look for a Retintopy folder within
> >> /Retinotopy/3/. I suppose the Retinotopy folder should be
> >> placed under freesurfer/subjects/ ? Am I missing something
> here?
> >>

[Freesurfer] Correcting left-right flip for multiple subjects at the same timepoint

[Chiu, Bryan (PHTH)]

Hi,

I'm attempting to do some longitudinal processing on a set of data with 
subjects with up to 4 timepoint scans: Baseline, Midpoint, Final, 12 months 
after Final.

When visually checking over a subject in Freeview, I notice that all of my 
Midpoint runs are left-right flipped, where the other 3 timepoints' scans are 
congruent with one another.

What can I do to flip these Midpoint volumes left-right before I rerun them all 
in recon-all "-all"?

As well, since these are going to the same subjects for my longitudinal design 
in creating a 'base' file we have to ensure that we maintain the same 
orientation of the brain across all timepoints (left-right)?

Thanks in advance,

- Bryan
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Re: [Freesurfer] Correcting left-right flip for multiple subjects at the same timepoint

[Douglas N Greve]

How did you convert to mgz? Did you start with dicoms and use 
mri_convert? How do you know they are flipped?



On 06/23/2014 12:56 PM, Chiu, Bryan (PHTH) wrote:
> Hi,
>
> I'm attempting to do some longitudinal processing on a set of data 
> with subjects with up to 4 timepoint scans: Baseline, Midpoint, Final, 
> 12 months after Final.
>
> When visually checking over a subject in Freeview, I notice that all 
> of my Midpoint runs are left-right flipped, where the other 3 
> timepoints' scans are congruent with one another.
>
> What can I do to flip these Midpoint volumes left-right before I rerun 
> them all in recon-all "-all"?
>
> As well, since these are going to the same subjects for my 
> longitudinal design in creating a 'base' file we have to ensure that 
> we maintain the same orientation of the brain across all timepoints 
> (left-right)?
>
> Thanks in advance,
>
> - Bryan
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] A comparison between atlases

[Dorian P.]

Dear Freesurfer followers/developers,

I am doing a study involving temporal lobes and the parcellations from
Desikan and Destrieux atlases have very different results. I like the full
gyrus parcellation of Desikan but the temporal pole is very small and
limited, while in Destriux the temporal pole is bigger and more appropriate
to be studied separately. My question is: can I combine parcellations from
these atlases? I.e., if I subtract the temporal pole from Destriuex from
the map of Desikan, will I take off all the anterior temporal pole gray
matter, or is there any potential mismatch between parcellations so there
will remain voxels in the anterior temporal lobe?

Thank you.

P.s. One less important question I have is this. I have noticed that
wmparc.mgz is the same as aparc+aseg.mgz with the addition of white matter
parcels. For Destrieux there is only the aparc.a2009s+aseg.mgz. Does this
file  have also the WM parcellation?
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[Freesurfer] Fwd: surface to volume visualization

[james pardon]

Sorry if you are receiving this for the second time , not really sure if
this went through the first time I sent the email:


Dear all,

I'm looking for a way to automate surface on volume visualization, to check
if the surface reconstruction have been successful on a very large number
of subjects. Normally, I would use freeview with -f and -v flags to check
and see if it is necessary to edit controls points, etc.

As an example, one option to automate this process is to use freeview
snapshot option and write a script that runs on several hundred subjects
and then show all the resulting images in html format.  Running freeview
with snapshot option works really good, however, since every freeview run
needs X11 there is an overhead here, especially when I'm running on a
remote cluster with no X11, which makes running X11 almost impossible.

I'm wondering whether any one has a better idea for this?

Thanks
James
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Re: [Freesurfer] Why the result was not same for the same subject

[Chiu, Bryan (PHTH)]

There of course is some variability in the analysis due to the way the 
segmentation happens. Your results are certainly not out of the ordinary for 
the volume you are viewing. On average you can expect a ~1% variance between 
several scans of the same subject.

If you want to know more I certainly suggest reading the paper titled: "Whole 
Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the 
Human Brain"

- Bryan


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Re: [Freesurfer] Extracting mean diffusivity values from diffusion data in freesurfer 5.3

[Douglas N Greve]

Was this ever answered?

1. Units - Not sure what the units of MD are. It might depend on your 
b-value
2. MD is not constrained to be between 0 and 1. Where are you getting that?
3. I don't know about the CC values. The CC ROIs are pretty small, and 
you might be getting significant partial voluming

doug

On 06/06/2014 02:06 AM, Rotem Saar wrote:
> Dear freesurfer experts,
>
> I'm using freesurfer 5.3 for extracting FA and MD values for each 
> region from the *aseg file for each subject.
> While I get validated FA values (I validated them with you, the 
> literature and some other software I used), I have a problem getting 
> reasonable MD values.
>
> This is the script I'm using for extracting the MD values:
>
> 1) dt_recon --i 
> /usr/local/freesurfer/subjects/Anatomy0981/DTI/I160.dcm --s 
> Anatomy0981 --o /usr/local/freesurfer/subjects/Anatomy0981/DTI --b 
> /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvals.bval 
> /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvecs.bvec
>
> 2) mri_label2vol --seg 
> /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --temp 
> /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --reg 
> /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --o 
> /usr/local/freesurfer/subjects/Anatomy0981/DTI/forMD.mgz
>
> 3) mri_segstats --seg-erode 1 --seg 
> /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --ctab 
> $FREESURFER_HOME/FreeSurferColorLUT.txt --i 
> /usr/local/freesurfer/subjects/Anatomy0981/DTI/forMD.mgz --sum 
> /usr/local/freesurfer/subjects/Anatomy0981/stats/all_stats_MD-masked
>
> It writes *.txt files similar to the ones of the FA (and also the 
> volumetric analysis) which is good, but -
>
> 1) I can't understand the units (it is written "unknown"). can u tell 
> me what do these units refer to ?
> 2) I can't understand why the units I get don't corresponds to the 
> units in the literature (0-1). Is there a transformation I need to 
> apply to these units in order to get the values we all see in the 
> literature (MD values ranges between 0 to 1 in the papers I read).
> 3) I am concerned about the differences in the values both between and 
> within subjects. For example, see 3 different subjects and their MD 
> values for the corpus-callosum:
>
> subject 1:
>
>  35 251   368  368.0 CC_Posterior   
> 7.4783 7.9938 0.16.16.
>  36 252   110  110.0 CC_Mid_Posterior  
> 56.7273   476.3758 0.  5002.  5002.
>  37 253   205  205.0  CC_Central 992.4537  1806.8883 
> 0.  5002.  5002.
>  38 254   132  132.0  CC_Mid_Anterior 1664.2954  2328.8467
> 43.  5002.  4959.
>  39 255   277  277.0  CC_Anterior 1723.4620  1914.7883 
> 0.  5002.  5002.
>
> subject 2:
>
>  36 251   328  328.0 CC_Posterior   
> 0. 0. 0. 0. 0.
>  37 25278   78.0 CC_Mid_Posterior  
> 43.9744   226.6371 0.  2000.  2000.
>  38 253   100  100.0  CC_Central 203.0800   779.8602 
> 0.  5001.  5001.
>  39 25483   83.0  CC_Mid_Anterior 264.5783   364.1581 
> 0.  1002.  1002.
>  40 255   321  321.0  CC_Anterior 985.8879   720.5300 
> 0.  3028.  3028.
>
> subject 3:
>
>  35 251   424  424.0 CC_Posterior  
> 20.6840 6.6236 10.60.50.
>  36 252   160  160.0  CC_Mid_Posterior 143.4312   780.4187 
> 0.  5001.  5001.
>  37 253   202  202.0  CC_Central 538.0248  1143.9441 
> 0.  5001.  5001.
>  38 254   179  179.0  CC_Mid_Anterior 496.5140   623.4088 
> 0.  2023.  2023.
>  39 255   361  361.0  CC_Anterior 211.6094   539.0007 
> 0.  2028.  2028.
>
> the values are really different both within the CC parts of the same 
> subject (does this make any sense ??) and also between subjects...
>
> We ruled out a problem in the gradient matrix (both with you and 
> because the FA values corresponds to reasonable values both from the 
> literature and other software we use).
>
> Can u please advise on how can we solve this issue ? We are in the 
> middle of submission of a very novel study and were required to show 
> addition analysis of the MD values - this is why this is so impotent 
> to us. Attached please find the full *.txt files I got.
>
> Thanks for your help.
>
> Rotem Saar-Ashkenazy
>
> Department of Brain and Cognitive Science
> Ben Gurion University of the Negev, Beer-Sheva, 84105
>
> School of Social Work
> Ashkelon Academic College, Ashkelon, 78211
>
> Israel
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone

Re: [Freesurfer] A comparison between atlases

[Bruce Fischl]

Hi Dorian

you don't need to combine them in any specific way if all you want is to 
look at ROI-based stats. Just take the ones from each atlas that you 
like.


cheers
Bruce
On Mon, 23 Jun 2014, Dorian P. wrote:


Dear Freesurfer followers/developers,
I am doing a study involving temporal lobes and the parcellations from
Desikan and Destrieux atlases have very different results. I like the full
gyrus parcellation of Desikan but the temporal pole is very small and
limited, while in Destriux the temporal pole is bigger and more appropriate
to be studied separately. My question is: can I combine parcellations from
these atlases? I.e., if I subtract the temporal pole from Destriuex from the
map of Desikan, will I take off all the anterior temporal pole gray matter,
or is there any potential mismatch between parcellations so there will
remain voxels in the anterior temporal lobe?

Thank you.

P.s. One less important question I have is this. I have noticed that
wmparc.mgz is the same as aparc+aseg.mgz with the addition of white matter
parcels. For Destrieux there is only the aparc.a2009s+aseg.mgz. Does this
file  have also the WM parcellation?



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Re: [Freesurfer] Fwd: surface to volume visualization

[Bruce Fischl]

Hi James

Ruopeng is traveling and may not answer quickly, although Louis might be 
able to help

Bruce
On Mon, 23 Jun 2014, james pardon wrote:


Sorry if you are receiving this for the second time , not really sure if
this went through the first time I sent the email:


Dear all, 
I'm looking for a way to automate surface on volume visualization, to check
if the surface reconstruction have been successful on a very large number of
subjects. Normally, I would use freeview with -f and -v flags to check and
see if it is necessary to edit controls points, etc. 

As an example, one option to automate this process is to use freeview
snapshot option and write a script that runs on several hundred subjects and
then show all the resulting images in html format.  Running freeview with
snapshot option works really good, however, since every freeview run needs
X11 there is an overhead here, especially when I'm running on a remote
cluster with no X11, which makes running X11 almost impossible. 

I'm wondering whether any one has a better idea for this? 

Thanks
James


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Re: [Freesurfer] Why the result was not same for the same subject

[Harms, Michael]

Actually, if you run 'recon-all' a second time (from scratch) on the same
subject, on the same platform/architecture, and you use the default
recon-all settings (i.e., don't use the -randomness flag, or specify your
random seed via the -rng-seed flag), then you should get identical
results, because for quite a few versions now, recon-all has been set up
to use the same random seed (1234) in all the binaries that involve
randomness.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 6/23/14 12:05 PM, "Chiu, Bryan (PHTH)"  wrote:

>There of course is some variability in the analysis due to the way the
>segmentation happens. Your results are certainly not out of the ordinary
>for the volume you are viewing. On average you can expect a ~1% variance
>between several scans of the same subject.
>
>If you want to know more I certainly suggest reading the paper titled:
>"Whole Brain Segmentation: Automated Labeling of Neuroanatomical
>Structures in the Human Brain"
>
>- Bryan
>
>
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>The information in this e-mail is intended only for the person to whom it
>is
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>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] A comparison between atlases

[Douglas N Greve]

 >>For Destrieux there is only the aparc.a2009s+aseg.mgz. Does this file 
  have also the WM parcellation?

Not by default, bu you can create one easily enough with

cd $SUBJECTS_DIR/subject
mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown 
--volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg aparc.a2009s+aseg.mgz

doug

On 06/23/2014 01:03 PM, Dorian P. wrote:
> Dear Freesurfer followers/developers,
>
> I am doing a study involving temporal lobes and the parcellations from 
> Desikan and Destrieux atlases have very different results. I like the 
> full gyrus parcellation of Desikan but the temporal pole is very small 
> and limited, while in Destriux the temporal pole is bigger and more 
> appropriate to be studied separately. My question is: can I combine 
> parcellations from these atlases? I.e., if I subtract the temporal 
> pole from Destriuex from the map of Desikan, will I take off all the 
> anterior temporal pole gray matter, or is there any potential mismatch 
> between parcellations so there will remain voxels in the anterior 
> temporal lobe?
>
> Thank you.
>
> P.s. One less important question I have is this. I have noticed that 
> wmparc.mgz is the same as aparc+aseg.mgz with the addition of white 
> matter parcels. For Destrieux there is only the aparc.a2009s+aseg.mgz. 
> Does this file  have also the WM parcellation?
>
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Why the result was not same for the same subject

[Bruce Fischl]

yes, that was our goal some time ago and we thought we had succeeded in 
tracking down and fixing any randomness if the same seed is specified

Bruce


On Mon, 23 Jun 2014, Harms, Michael wrote:

>
> Actually, if you run 'recon-all' a second time (from scratch) on the same
> subject, on the same platform/architecture, and you use the default
> recon-all settings (i.e., don't use the -randomness flag, or specify your
> random seed via the -rng-seed flag), then you should get identical
> results, because for quite a few versions now, recon-all has been set up
> to use the same random seed (1234) in all the binaries that involve
> randomness.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.   Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
> On 6/23/14 12:05 PM, "Chiu, Bryan (PHTH)"  wrote:
>
>> There of course is some variability in the analysis due to the way the
>> segmentation happens. Your results are certainly not out of the ordinary
>> for the volume you are viewing. On average you can expect a ~1% variance
>> between several scans of the same subject.
>>
>> If you want to know more I certainly suggest reading the paper titled:
>> "Whole Brain Segmentation: Automated Labeling of Neuroanatomical
>> Structures in the Human Brain"
>>
>> - Bryan
>>
>>
>> ___
>> 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.
>>
>
>
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.
>
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[Freesurfer] QDEC Error loading the data table

[Mohammed Goryawala]

Hello FreeSurfer Experts,

I am trying to run QDEC for a group comparison study. I am following the
tutorial found on
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview

However, when I try to load my data table it returns the error.


Loading data table /home/pcopy_project/qdec/qdec.table.dat...
Number of columns:  5
fsid column:1
Number of factors:  4
Number of subjects: 57
Reading discrete factor levels from config file
/home/pcopy_project/qdec/gender.levels
Female
Male
done.
Reading discrete factor levels from config file
/home/pcopy_project/qdec/diagnosis.levels
Control
Disease
done.

ERROR: Subject SIYA_001 has an invalid level 'Male' in the gender column
INFO: If 'gender' is a discrete factor, then create a file
named 'gender.levels' containing the valid factor names
one per line.
Error loading the data table.


As you see I have a 'gender.levels' file in the same directory as the data
file and it reads it above. I still get the error.

I am new to QDEC and any help would be appreciated.

Thank you
Mohammed Goryawala, PhD
Research Associate
Department of Radiology
University of Miami Miller School of Medicine
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Re: [Freesurfer] A comparison between atlases

[Dorian P.]

Thank you Bruce and Douglas,

I meant to combine them because I did not want overlaps.

Can I advance one more question as we are here. How can I get an average
thickness of the entire lateral temporal lobe (inferior, medial, temporal
gyri)? The average of the three gyri may not be useful as one gyrus may be
bigger and should be counted accordingly in the average thickness of the
entire lateral part.

Thank you.


2014-06-23 13:22 GMT-04:00 Douglas N Greve :

>  >>For Destrieux there is only the aparc.a2009s+aseg.mgz. Does this file
>   have also the WM parcellation?
>
> Not by default, bu you can create one easily enough with
>
> cd $SUBJECTS_DIR/subject
> mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown
> --volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg aparc.a2009s+aseg.mgz
>
> doug
>
> On 06/23/2014 01:03 PM, Dorian P. wrote:
> > Dear Freesurfer followers/developers,
> >
> > I am doing a study involving temporal lobes and the parcellations from
> > Desikan and Destrieux atlases have very different results. I like the
> > full gyrus parcellation of Desikan but the temporal pole is very small
> > and limited, while in Destriux the temporal pole is bigger and more
> > appropriate to be studied separately. My question is: can I combine
> > parcellations from these atlases? I.e., if I subtract the temporal
> > pole from Destriuex from the map of Desikan, will I take off all the
> > anterior temporal pole gray matter, or is there any potential mismatch
> > between parcellations so there will remain voxels in the anterior
> > temporal lobe?
> >
> > Thank you.
> >
> > P.s. One less important question I have is this. I have noticed that
> > wmparc.mgz is the same as aparc+aseg.mgz with the addition of white
> > matter parcels. For Destrieux there is only the aparc.a2009s+aseg.mgz.
> > Does this file  have also the WM parcellation?
> >
> >
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
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>
>
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> is
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> e-mail
> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] QDEC Error loading the data table

[Douglas N Greve]

That does look pretty silly. How did you create your qdec.table.dat and 
level files? If you created them under windows, then that could be the 
problem. If not, post your qdec.table.dat file and the gender.level file 
and I'll take a look

On 06/23/2014 01:33 PM, Mohammed Goryawala wrote:
> Hello FreeSurfer Experts,
>
> I am trying to run QDEC for a group comparison study. I am following 
> the tutorial found on 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview
>
> However, when I try to load my data table it returns the error.
>
> 
> Loading data table /home/pcopy_project/qdec/qdec.table.dat...
> Number of columns:  5
> fsid column:1
> Number of factors:  4
> Number of subjects: 57
> Reading discrete factor levels from config file 
> /home/pcopy_project/qdec/gender.levels
> Female
> Male
> done.
> Reading discrete factor levels from config file 
> /home/pcopy_project/qdec/diagnosis.levels
> Control
> Disease
> done.
>
> ERROR: Subject SIYA_001 has an invalid level 'Male' in the gender column
> INFO: If 'gender' is a discrete factor, then create a file
> named 'gender.levels' containing the valid factor names
> one per line.
> Error loading the data table.
> 
>
> As you see I have a 'gender.levels' file in the same directory as the 
> data file and it reads it above. I still get the error.
>
> I am new to QDEC and any help would be appreciated.
>
> Thank you
> Mohammed Goryawala, PhD
> Research Associate
> Department of Radiology
> University of Miami Miller School of Medicine
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] A comparison between atlases

[Douglas N Greve]

On 06/23/2014 01:35 PM, Dorian P. wrote:
> Thank you Bruce and Douglas,
>
> I meant to combine them because I did not want overlaps.
I don't think we have any tools to mix and match them.
>
> Can I advance one more question as we are here. How can I get an 
> average thickness of the entire lateral temporal lobe (inferior, 
> medial, temporal gyri)? The average of the three gyri may not be 
> useful as one gyrus may be bigger and should be counted accordingly in 
> the average thickness of the entire lateral part.
You can create a new annotation of the major lobes with

mri_annotation2label --subject $subject --hemi $hemi --lobesStrict lobes
This creates ?h.lobes.annot

doug


>
> Thank you.
>
>
> 2014-06-23 13:22 GMT-04:00 Douglas N Greve  >:
>
>  >>For Destrieux there is only the aparc.a2009s+aseg.mgz. Does
> this file
>   have also the WM parcellation?
>
> Not by default, bu you can create one easily enough with
>
> cd $SUBJECTS_DIR/subject
> mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown
> --volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg
> aparc.a2009s+aseg.mgz
>
> doug
>
> On 06/23/2014 01:03 PM, Dorian P. wrote:
> > Dear Freesurfer followers/developers,
> >
> > I am doing a study involving temporal lobes and the
> parcellations from
> > Desikan and Destrieux atlases have very different results. I
> like the
> > full gyrus parcellation of Desikan but the temporal pole is very
> small
> > and limited, while in Destriux the temporal pole is bigger and more
> > appropriate to be studied separately. My question is: can I combine
> > parcellations from these atlases? I.e., if I subtract the temporal
> > pole from Destriuex from the map of Desikan, will I take off all the
> > anterior temporal pole gray matter, or is there any potential
> mismatch
> > between parcellations so there will remain voxels in the anterior
> > temporal lobe?
> >
> > Thank you.
> >
> > P.s. One less important question I have is this. I have noticed that
> > wmparc.mgz is the same as aparc+aseg.mgz with the addition of white
> > matter parcels. For Destrieux there is only the
> aparc.a2009s+aseg.mgz.
> > Does this file  have also the WM parcellation?
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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.
>
>
>
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] RAS to voxel transform

[Arman Eshaghi]

Hi,

I'm trying to understand the conversion from RAS (freesurfer surface
coordinate) to volume space (x, y, and z.. According to Graham Wideman
documentation here
http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm (if it is not
outdated), Right is negative x, *Anterior is positive z*, and *Superior is
positive y*.

Just to double check, usign mri_info on a sample T1.mgz in one subject I
get this ras to voxel transform:

-1   00   126.944
 0   0   -1   135.16
 0   10   110.6
 0   001

Assuming we have correctly set the (0, 0, 0), and we can extract R A and S
(respectively) coordinates using C++ or Python code it means: Right is
negative x, *Anterior is negative z*, and *Superior is positive y*
(conflicting coordinates are in vold). Am I missing anything here, or
coordinate systems have changed from the probably outdated documentation?
Thanks in advance for any input on this rather confusing point.

All the best,
Arman
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Re: [Freesurfer] QDEC Error loading the data table

[Mohammed Goryawala]

Hi Doug,

I did create them in windows. I will recreate them on the linux machine and
carry out the processing.

Thanks for the help.
Mohammed


On Mon, Jun 23, 2014 at 1:38 PM, Douglas N Greve 
wrote:

>
> That does look pretty silly. How did you create your qdec.table.dat and
> level files? If you created them under windows, then that could be the
> problem. If not, post your qdec.table.dat file and the gender.level file
> and I'll take a look
>
> On 06/23/2014 01:33 PM, Mohammed Goryawala wrote:
> > Hello FreeSurfer Experts,
> >
> > I am trying to run QDEC for a group comparison study. I am following
> > the tutorial found on
> >
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview
> >
> > However, when I try to load my data table it returns the error.
> >
> > 
> > Loading data table /home/pcopy_project/qdec/qdec.table.dat...
> > Number of columns:  5
> > fsid column:1
> > Number of factors:  4
> > Number of subjects: 57
> > Reading discrete factor levels from config file
> > /home/pcopy_project/qdec/gender.levels
> > Female
> > Male
> > done.
> > Reading discrete factor levels from config file
> > /home/pcopy_project/qdec/diagnosis.levels
> > Control
> > Disease
> > done.
> >
> > ERROR: Subject SIYA_001 has an invalid level 'Male' in the gender column
> > INFO: If 'gender' is a discrete factor, then create a file
> > named 'gender.levels' containing the valid factor names
> > one per line.
> > Error loading the data table.
> > 
> >
> > As you see I have a 'gender.levels' file in the same directory as the
> > data file and it reads it above. I still get the error.
> >
> > I am new to QDEC and any help would be appreciated.
> >
> > Thank you
> > Mohammed Goryawala, PhD
> > Research Associate
> > Department of Radiology
> > University of Miami Miller School of Medicine
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] RAS to voxel transform

[Douglas N Greve]

Your interpretation is not correct. RAS always means that R is pos x, A 
is pos y, and S is pos z.

That is the voxel-to-RAS transform. Here voxel means column-row-slice. 
So this matrix takes a col, row, slice and converts it into a RAS. So 
that first negative 1 means that as the column number increases the R 
decreases (ie, becomes more leftward)

Look at our wiki 
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems for more info

doug



On 06/23/2014 01:44 PM, Arman Eshaghi wrote:
> Hi,
>
> I'm trying to understand the conversion from RAS (freesurfer surface 
> coordinate) to volume space (x, y, and z.. According to Graham Wideman 
> documentation here 
> http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm (if it is 
> not outdated), Right is negative x, *Anterior is positive z*, and 
> *Superior is positive y*.
>
> Just to double check, usign mri_info on a sample T1.mgz in one subject 
> I get this ras to voxel transform:
>
> -1   00   126.944
>  0   0   -1   135.16
>  0   10   110.6
>  0   001
>
> Assuming we have correctly set the (0, 0, 0), and we can extract R A 
> and S (respectively) coordinates using C++ or Python code it means: 
> Right is negative x, *Anterior is negative z*, and *Superior is 
> positive y* (conflicting coordinates are in vold). Am I missing 
> anything here, or coordinate systems have changed from the probably 
> outdated documentation? Thanks in advance for any input on this rather 
> confusing point.
>
> All the best,
> Arman
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Fwd: mpr2mni305 failed, see transforms/talairach_avi.log

[Nick Schmansky, MGH]

Venkat,

Can you send me your orig.mgz so that I can attempt to replicate?

Nick
  

On Mon, 2014-06-23 at 08:46 +0530, Venkateswaran Rajagopalan wrote:
> Hi Bruce,
> 
> 
> Thanks very much. I will wait for Avi Synder's response.
> 
> 
> Thanks a lot
> Venkat
> 
> 
> On Sat, Jun 21, 2014 at 8:23 PM, Bruce Fischl
>  wrote:
> Hi  Venkat
> 
> I'll cc Avi Snyder. Avi: do you know what this error message
> means?
> 
> thanks
> Bruce
> 
> 
> On Sat, 21 Jun 2014, Venkateswaran Rajagopalan wrote:
> 
> Dear All,
> 
> I am sorry to post this again. Any help will be
> greatly appreciated. I am
> struck as I am unable to run the recon-all step.
> 
> Thanks
> Venkat
> 
> -- Forwarded message --
> From: Venkateswaran Rajagopalan
> 
> Date: Fri, Jun 20, 2014 at 5:14 PM
> Subject: mpr2mni305 failed, see
> transforms/talairach_avi.log
> To: Freesurfer support list
> 
> 
> 
> Hi All,
> 
> I am getting the the following error when I run
> recon-all -subjid E368
> -autorecon1
> 
> ERROR: mpr2mni305 failed, see
> transforms/talairach_avi.log
> 
> Here is what talairach_avi.log says
> 
> /home/administrator/Desktop/freesurfer/subjects_dir/E368/mri
> /usr/local/freesurfer/bin/talairach_avi
> --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
> $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp
> $
> Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic
> #46-Ubuntu SMP Thu Apr
> 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux
> Fri Jun 20 17:06:38 IST 2014
> mri_convert orig_nu.mgz talsrcimg.img
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
> mreuter Exp $
> reading from orig_nu.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> writing to talsrcimg.img...
> Analyze Output Matrix
> -1.000   0.000   0.000   129.000;
>  0.000   0.000   1.000  -129.000;
>  0.000  -1.000   0.000   122.500;
>  0.000   0.000   0.000   1.000;
> 
> INFO: set hdr.hist.orient to -1
> mpr2mni305 talsrcimg
> Fri Jun 20 17:06:39 IST 2014
> /usr/local/freesurfer/bin/mpr2mni305 talsrcimg
> $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $
> target=711-2C_as_mni_average_305
> 
> 
> -
> analyzeto4dfp talsrcimg -O0 -y
> 
> -
> 
> $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $
> Fri Jun 20 17:06:40 2014
> Writing: talsrcimg.4dfp.hdr
> $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks
> Exp $
> Reading: talsrcimg.hdr
> header size 348 bytes
> hdr.dime.datatypeoffset=70value=2
> hdr.dime.bitpixoffset=72value=8
> hdr.hist.orientoffset=252value=-1
> dimensionality 4
> dimensions   256   256   256 1
> Reading: talsrcimg.img
> Writing: talsrcimg.4dfp.img
> Writing: talsrcimg.4dfp.ifh
> ifh2hdr talsrcimg -r0to255
> ori=2
> 
> 
> -
> gauss_4dfp talsrcimg 1.1
> 
> -
> 
> $Id: gauss_4dfp.c,v 1.3 2009/05/15 21:43:46 nicks Exp
> $
> Reading: talsrcimg.4dfp.img
> Writing: talsrcimg_g11.4dfp.img
> image dimensions 256 256 256 padded to 288 288 288
> processing volume 1$Id: ifh2hdr.c,v 1.3 2007/05/05
> 10:45:03 nicks Exp $
> Fri Jun 20 17:06:46 2014
> 

Re: [Freesurfer] hippocampal subfields in young subjects

[Joana Braga Pereira]

Dear Koen and Freesurfers,

I haven't receive any further replies regarding the black lines surrounding
the subfields I found in the sample of subjects I am analyzing.

As I said the subjects are quite young (9-14 years of age) and I visualized
the subfields with Freeview.

Do you have any idea why this is happening? This does mean the GEMS tool
should not be applied in such young subjects?

Any help would be greatly appreciated!

Many thanks,

joana




2014-06-13 15:40 GMT+02:00 Joana Braga Pereira :

> Hi Koen,
>
> Thanks for such a prompt reply.
>
> I visualized it in freeview with:
>
> freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz
> -p-labels posterior_right* posterior_Right-Hippocampus.mgz -p-prefix
> posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt
>
> Thanks,
>
> Joana
>
>
> 2014-06-13 15:23 GMT+02:00 Koen Van Leemput :
>
> Hi Joana,
>>
>> This looks like a visualization issue rather than a segmentation error to
>> me. How did you visualize this?
>>
>> Koen
>>  On Jun 13, 2014 2:59 PM, "Joana Braga Pereira" 
>> wrote:
>>
>>> Dear all,
>>>
>>> I'm running the GEMS tool in Freesurfer 5.3 to measure the volumes of
>>> hippocampal subfields in subjects between 9 and 14 years of age with 3T
>>> T1-weighted MRI scans.
>>>
>>> I noticed that a blackline is consistently drawn around the surface of
>>> the subfields (see attached figure) and was wondering whether this is
>>> normal.
>>>
>>> Since the tool has not been validated in young subjects I would like to
>>> know if the black line observed in the figure shows that the segmentation
>>> has not been carried out correctly.
>>>
>>> Any help will be greatly appreciated.
>>>
>>> Many thanks,
>>>
>>> Joana
>>>
>>> ___
>>> 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
>>
>>
>> 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] recon-all ERROR, no idea why

[Remy Wahnoun]

Thanks Douglas,

I definitely appreciate your help.

Here is what it Spit out,



*Rémy Wahnoun, PhD*

Biomedical Research Group Manager

Barrow Neurological Institute at Phoenix Children's Hospital

Adjunct Faculty, Arizona State University

*www.NeuralControl.net *





set echo = 1 ;

set debug = 1 ;

set debug = 1

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 11 != 0 )



set flag = $argv[1] ; shift ;

set flag = --n

shift



switch ( $flag )

switch ( --n )

if ( $#argv == 0 ) goto arg1err ;

if ( 10 == 0 ) goto arg1err

set nIters = $argv[1] ; shift ;

set nIters = 1

shift

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 9 != 0 )



set flag = $argv[1] ; shift ;

set flag = --proto-iters

shift



switch ( $flag )

switch ( --proto-iters )

if ( $#argv == 0 ) goto arg1err ;

if ( 8 == 0 ) goto arg1err

set nProtoIters = $argv[1] ; shift ;

set nProtoIters = 1000

shift

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 7 != 0 )



set flag = $argv[1] ; shift ;

set flag = --distance

shift



switch ( $flag )

switch ( --distance )

if ( $#argv == 0 ) goto arg1err ;

if ( 6 == 0 ) goto arg1err

set Distance = $argv[1] ; shift ;

set Distance = 50

shift

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 5 != 0 )



set flag = $argv[1] ; shift ;

set flag = --no-rescale

shift



switch ( $flag )

switch ( --no-rescale )

set DoRescale = 0 ;

set DoRescale = 0

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 4 != 0 )



set flag = $argv[1] ; shift ;

set flag = --i

shift



switch ( $flag )

switch ( --i )

if ( $#argv == 0 ) goto arg1err ;

if ( 3 == 0 ) goto arg1err

set InVol = $argv[1] ; shift ;

set InVol = orig.mgz

shift

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 2 != 0 )



set flag = $argv[1] ; shift ;

set flag = --o

shift



switch ( $flag )

switch ( --o )

if ( $#argv == 0 ) goto arg1err ;

if ( 1 == 0 ) goto arg1err

set OutVol = $argv[1] ; shift ;

set OutVol = orig_nu.mgz

shift

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 0 != 0 )



goto parse_args_return ;

goto parse_args_return





goto check_params ;

goto check_params

if ( $#InVol == 0 ) then

if ( 1 == 0 ) then

if ( ! -e $InVol ) then

if ( ! -e orig.mgz ) then

if ( $#OutVol == 0 ) then

if ( 1 == 0 ) then



goto check_params_return ;

goto check_params_return



set OutDir = `dirname $OutVol` ;

set OutDir = `dirname $OutVol`

dirname orig_nu.mgz

mkdir -p $OutDir ;

mkdir -p .



if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log

if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log

set LF = ./mri_nu_correct.mni.log

if ( -e $LF ) mv $LF $LF.bak

if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log
./mri_nu_correct.mni.log.bak

mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak



pwd | tee -a $LF

pwd

tee -a ./mri_nu_correct.mni.log

/media/sf_Imagery/FreeSurfer/xx/mri

which mri_nu_correct.mni | tee -a $LF

which mri_nu_correct.mni

tee -a ./mri_nu_correct.mni.log

/usr/local/freesurfer/bin/mri_nu_correct.mni

echo $cmdargs | tee -a $LF

echo --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
orig.mgz --o orig_nu.mgz

tee -a ./mri_nu_correct.mni.log

--debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz
--o orig_nu.mgz

echo "nIters $nIters" | tee -a $LF

echo nIters 1

tee -a ./mri_nu_correct.mni.log

nIters 1

echo $VERSION | tee -a $LF

tee -a ./mri_nu_correct.mni.log

echo $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $

$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $

uname -a | tee -a $LF

uname -a

tee -a ./mri_nu_correct.mni.log

Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48
UTC 2014 i686 i686 i386 GNU/Linux

date | tee -a $LF

date

tee -a ./mri_nu_correct.mni.log

Mon Jun 23 15:32:45 EDT 2014

nu_correct -version | tee -a $LF

nu_correct -version

tee -a ./mri_nu_correct.mni.log

Program nu_correct, built from:

Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu)
on 2010-02-20 at 20:19:13



if ( ! $#tmpdir ) set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$

if ( ! 0 ) set tmpdir = ./tmp.mri_nu_correct.mni.1745

set tmpdir = ./tmp.mri_nu_correct.mni.1745

mkdir -p $tmpdir

mkdir -p ./tmp.mri_nu_correct.mni.1745

echo "tmpdir is $tmpdir" | tee -a $LF

echo tmpdir is ./tmp.mri_nu_correct.mni.1745

tee -a ./mri_nu_correct.mni.log

tmpdir is ./tmp.mri_nu_correct.mni.1745





set cmd = ( mri_convert ${HiRes} $InVol $tmpdir/nu0.mnc )

set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc )

if ( $UseFloat ) set cmd = ( $cmd -odt float )

if ( 1 ) set cmd = ( mri_convert orig.mgz
./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float )

set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt
float )

pwd | & tee -a $LF

pwd

tee -a ./mri_nu_correct.mni.log

/media/sf_Imagery/FreeSurfer/xx/mri

echo $cmd | & tee -a 

[Freesurfer] fMRI Image Acquisition and Analyses Course : October 16-18, 2014 (fwd)

[Bruce Fischl]

FYI

--

The Mind Research Network (MIND) is pleased to invite you
​​to the fMRI Image Acquisition and Analyses Course held on October 16-18,
2014 on the campus of the University of New Mexico in Albuquerque, New
Mexico.

For more information and registration, see
http://www.mrn.org/education-outreach/courses-and-events/

Special topics include the unique issues that multiband EPI (i.e., whole
brain subsecond EPI) brings to fMRI analyses


***Email Kent A. Kiehl kki...@unm.edu or fmricou...@mrn.org with any
questions.


We hope to see you there. Thanks for your time, and have a great day!
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] problem with qdec stats tables

[Kristina Kuhlmann]

Dear mailing-list,

I’ve got a question concerning the file types of stats tables in qdec. After generating the stats tables there are two files e.g. lh.aparc.a2005s.area.stats and lh.aparc.area.stats. Which one is the right one to work with ( statistical analysis)? How do they differ in characteristics and values?

 

Thanks,

best regards, Kristina

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

Re: [Freesurfer] Fwd: mpr2mni305 failed, see transforms/talairach_avi.log

[Venkateswaran Rajagopalan]

Nick,

Thanks for your kind help. I uploaded my orig.mgz i.e. 001.mgz using
Martinos center file drop.

Thanks
Venkat


On Mon, Jun 23, 2014 at 11:42 PM, Nick Schmansky, MGH <
ni...@nmr.mgh.harvard.edu> wrote:

> Venkat,
>
> Can you send me your orig.mgz so that I can attempt to replicate?
>
> Nick
>
>
> On Mon, 2014-06-23 at 08:46 +0530, Venkateswaran Rajagopalan wrote:
> > Hi Bruce,
> >
> >
> > Thanks very much. I will wait for Avi Synder's response.
> >
> >
> > Thanks a lot
> > Venkat
> >
> >
> > On Sat, Jun 21, 2014 at 8:23 PM, Bruce Fischl
> >  wrote:
> > Hi  Venkat
> >
> > I'll cc Avi Snyder. Avi: do you know what this error message
> > means?
> >
> > thanks
> > Bruce
> >
> >
> > On Sat, 21 Jun 2014, Venkateswaran Rajagopalan wrote:
> >
> > Dear All,
> >
> > I am sorry to post this again. Any help will be
> > greatly appreciated. I am
> > struck as I am unable to run the recon-all step.
> >
> > Thanks
> > Venkat
> >
> > -- Forwarded message --
> > From: Venkateswaran Rajagopalan
> > 
> > Date: Fri, Jun 20, 2014 at 5:14 PM
> > Subject: mpr2mni305 failed, see
> > transforms/talairach_avi.log
> > To: Freesurfer support list
> > 
> >
> >
> > Hi All,
> >
> > I am getting the the following error when I run
> > recon-all -subjid E368
> > -autorecon1
> >
> > ERROR: mpr2mni305 failed, see
> > transforms/talairach_avi.log
> >
> > Here is what talairach_avi.log says
> >
> >
> /home/administrator/Desktop/freesurfer/subjects_dir/E368/mri
> > /usr/local/freesurfer/bin/talairach_avi
> > --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
> > $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp
> > $
> > Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic
> > #46-Ubuntu SMP Thu Apr
> > 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux
> > Fri Jun 20 17:06:38 IST 2014
> > mri_convert orig_nu.mgz talsrcimg.img
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
> > mreuter Exp $
> > reading from orig_nu.mgz...
> > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> > i_ras = (-1, 0, 0)
> > j_ras = (0, 0, -1)
> > k_ras = (0, 1, 0)
> > writing to talsrcimg.img...
> > Analyze Output Matrix
> > -1.000   0.000   0.000   129.000;
> >  0.000   0.000   1.000  -129.000;
> >  0.000  -1.000   0.000   122.500;
> >  0.000   0.000   0.000   1.000;
> > 
> > INFO: set hdr.hist.orient to -1
> > mpr2mni305 talsrcimg
> > Fri Jun 20 17:06:39 IST 2014
> > /usr/local/freesurfer/bin/mpr2mni305 talsrcimg
> > $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $
> > target=711-2C_as_mni_average_305
> >
> >
> -
> > analyzeto4dfp talsrcimg -O0 -y
> >
> -
> >
> > $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $
> > Fri Jun 20 17:06:40 2014
> > Writing: talsrcimg.4dfp.hdr
> > $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks
> > Exp $
> > Reading: talsrcimg.hdr
> > header size 348 bytes
> > hdr.dime.datatypeoffset=70value=2
> > hdr.dime.bitpixoffset=72value=8
> > hdr.hist.orientoffset=252value=-1
> > dimensionality 4
> > dimensions   256   256   256 1
> > Reading: talsrcimg.img
> > Writing: talsrcimg.4dfp.img
> > Writing: talsrcimg.4dfp.ifh
> > ifh2hdr talsrcimg -r0to255
> > ori=2
> >
> >
> -
> > gauss_4dfp talsrcimg 1.1
> >
> -
> >
> > $Id: gauss_4dfp.c,v 1.3 2009/05/15 21:43:46 nicks Exp
> > $
> > Reading: talsrcimg.4dfp.img
> > Writing: talsrcimg_g11.4dfp.img
> > image dimensions 256 256 256 padded to 288 288 288
> > processing volume 1$Id: ifh2hdr.c,v 1.3 2007