Re: [Freesurfer] "Bump" - Fwd: lGI value is aberrantly high and misalignment fix

mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Dear all, I have a problem with the LGI module. At the step when the software computes the LGIs for the vertices, In one vertex the lGI results aberrantly high and the software exits with ERRORS. I tried the solution sugges

Re: [Freesurfer] recon-all -lgi issue with MATLAB Student version - Help!

/SearchProjectionOnPial.m and make these changes: find this line: < for t=1:step:size(perim,2) and change to: > si=max(size(perim)); > for t=1:step:si Best, Marie On 05 Mar 2016, at 11:10, Marie Schaer <marie.sch...@unige.ch<mailto:marie.sch...@unige.ch>> wrote: Hi

Re: [Freesurfer] recon-all -lgi issue with MATLAB Student version - Help!

Hi Ankita, Did you get this error with only one subject, or with several different subjects? Have you checked your pial surface with freeview or tkmedit? No issue there? If your pial surfaces are fine and you get the issue for all the subjects you tried, send me a sample of pial surface +

Re: [Freesurfer] Calculating local gyrification using CIVET's surface file ('.obj')

Hi Kie Woo, The other thing that you might want to check is that the pial-outer-smoothed surface and the pial surface match, in case the transformation from the CIVET format induced any strange translation in space and they don't line up. Just open them both on a volume using tkmedit or

Re: [Freesurfer] pial_lgi option in qdec

Tara, After copying the .Qdecrc, did you check that the .Qdecrc file is in your home directory and that MEASURE1 = pial_lgi is listed there? When this is fine, start with a new terminal and pial_lgi should be in the option among other measures. Let me know, Marie On Sep 17, 2015, at 4:02

Re: [Freesurfer] pial_lgi option in qdec

5 at 6:09 PM, Marie Schaer <marie.sch...@unige.ch<mailto:marie.sch...@unige.ch>> wrote: Tara, After copying the .Qdecrc, did you check that the .Qdecrc file is in your home directory and that MEASURE1 = pial_lgi is listed there? When this is fine, start with a new terminal and pial_lgi

Re: [Freesurfer] surface area of outer smoothed hull

Hi Christiane, You can use mris_info lh.pial-outer-smoothed Best, Marie On Sep 7, 2015, at 10:57 PM, "Jockwitz, Christiane" > wrote: Dear all, I would like to extract the surface area from the outer smoothed hull of a particular

Re: [Freesurfer] Error running recon-all -localGI

://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting From: freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Marie Schaer marie.sch...@unige.chmailto:marie.sch

Re: [Freesurfer] Error running recon-all -localGI

Hi Philip, Can you send me the full recon-all.log for this subject so that I can see also matlab version and whether other vertices ran or if it crashed on the first one. Thanks, Marie On Aug 26, 2015, at 8:00 AM, Philip Deming pdem...@wisc.edumailto:pdem...@wisc.edu wrote: Hi Freesurfer

Re: [Freesurfer] Fwd: -qcache error

...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch Sent: Monday, May 4, 2015 2:39 PM To: Skyler Shollenbarger Cc: Freesurfer list Subject: Re: [Freesurfer] -qcache error Hi Skyler, (I added the freesurfer list in copy

Re: [Freesurfer] -qcache error

Hi Skyler, (I added the freesurfer list in copy, please post all your questions through the mailing list, thanks!) If the number of vertices does no match, it might be that you processed the LGI before you reprocessed the final version of the surfaces for which you completed the registration

Re: [Freesurfer] LGI problem

Hi Alan, Do you have the image processing toolbox installed in matlab? If not, I guess this is the source of the error. Best, Marie On Apr 30, 2015, at 7:51 AM, Alan Francis alandarkene...@gmail.commailto:alandarkene...@gmail.com wrote: Hi Marie: I am trying to run the LGI post processing

Re: [Freesurfer] lGI ?h.pial-outer-smoothed

. g.stripeik...@umcutrecht.nlmailto:g.stripeik...@umcutrecht.nl wrote: Hi Marie, Thanks for advice. I have attached a screenshot of overlaid lGI. I have at least 4 subjects with extremely high values of total 106. Best, Giedre From: Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch

Re: [Freesurfer] lGI ?h.pial-outer-smoothed

Hi Giedre, Small intersections like that are fine and won't affect the lGI computation, so you are good with that. Values around 20 are however more preoccupying! Can you send me a screenshot of the lGI overlaid on the surface for this subject using tksurfer or freeview? Best, Marie NB: if

[Freesurfer] obtaining the level of smoothness in the data

Hi all, I'd like to know whether there is a command line that I could use to extract the level of smoothness in my data, the same way qdec does it automatically, i.e. writing the fwhm.dat that is then used to define which precomputed CSD file should be used in the Monte Carlo Simulation. Is

Re: [Freesurfer] obtaining the level of smoothness in the data

--cortex --dat fwhm.dat doug On 12/11/14 8:40 PM, Marie Schaer wrote: Hi all, I'd like to know whether there is a command line that I could use to extract the level of smoothness in my data, the same way qdec does it automatically, i.e. writing the fwhm.dat that is then used to define which

Re: [Freesurfer] LGI analysis of single subject

Hi Maria, I have to say that I rarely use freeview, I prefer tkmedit and tksurfer that I know better. So I didn't realize that the images were shifted, I guess it's some preference in how to read the surface. I just tried and have the same kind of shift when using freeview, so I don't think

Re: [Freesurfer] LGI fails for fsaverage

Hi Pierre, I'm not sure exactly what you are trying to do, but it's true that LGI fails for fsaverage at the mris_fills step, where the volume looks cut. It seems to be something in the properties of the fsaverage surfaces. Maybe Doug or Bruce have an idea where it comes from. But in any

Re: [Freesurfer] GI analysis of single subject

Hi Maria, Here are the responses: 1. Can you send us a screenshot of what you mean with it doesn't hug the contours of the brain mask? You can use: tkmedit SUBJ T1.mgz lh.pial -aux-surface lh.pial-outer-smoothed (or the corresponding in freeview) and it should give you what correspond to the

Re: [Freesurfer] LGI fails for fsaverage

this? Thanks, Pierre On Oct 28, 2014 3:06 PM, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote: Hi Pierre, I'm not sure exactly what you are trying to do, but it's true that LGI fails for fsaverage at the mris_fills step, where the volume looks cut. It seems to be something

Re: [Freesurfer] LGI fails for fsaverage

/ editor - Follow us on Twitterhttp://twitter.com/PLOSNeuro Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitterhttp://twitter.com/pierre_vanmedge - Read my blog herehttp://neuroscimed.wordpress.com/ On Tue, Oct 28, 2014 at 5:23 PM, Marie Schaer marie.sch

Re: [Freesurfer] LGI Topological Defect

Hi Tara, Did you try to run the recon-all with the randomness flag? If you don't add this flag, your surfaces will not change much with the new recon-all and you'll probably get the same problem again when running LGI. Let me know if you still have trouble, Marie On Aug 22, 2014, at 7:07

Re: [Freesurfer] lobes gyrification

Hi Melly, You can use aparcstats2table from the file you created: aparcstats2table --subjects …. --hemi lh --meas thickness --parc aparc_lgi --t summary_lgi.txt Here you'll read the column thickness in the lh.aparc_lgi.stats file that you have created with mri_anatomical_stats (i.e.

Re: [Freesurfer] topological defects?

Hi Angela, Use mris_euler_number on the pial surface, but the probability that there will be any defect is indeed relatively low. Have you carefully checked your white and pial surface slice by slice overlaid on the T1? Sometimes a small region where the surfaces are wrinkled is responsible

Re: [Freesurfer] localGI - results interpretation

Hi Elisa, It is recommended to use lGI on a vertex-wise basis, i.e. to use qdec the same way you would for cortical thickness. To get access to pial_lgi as a measure of interest in qdec, you need to add a row with: MEASURE1 = pial_lgi in the .Qdecrc file located in your home directory.

Re: [Freesurfer] LocalGI error {Disarmed}

Hi Sarina, Thanks for the log, I see better the problem. However I unfortunately don't know the answer. The lGI calls MRIread and load_mgh, and the error seems to related to load_mgh.m itself. Bruce / Doug / Nick, any guess what can yield such a switch expression must be a scalar or string

Re: [Freesurfer] LocalGI error

Hi Sarina, Can you please send me the full log of the LGI (e.g. recon-all.log) for this subject? Thanks, Marie On Jul 28, 2014, at 7:23 AM, Sarina Iwabuchi sarina.iwabu...@nottingham.ac.ukmailto:sarina.iwabu...@nottingham.ac.uk wrote: Hi all, I have been trying to run localGI and have

Re: [Freesurfer] [Fwd: LGI recon problem]

Hi Angela, Have you tried that: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30506.html ? You can look also in the release notes (http://freesurfer.net/fswiki/ReleaseNotes), under LGI issue when using Matlab 2013. The issue will be corrected in the next FreeSurfer release.

Re: [Freesurfer] lobes gyrification

Hi Melly, The LGI has the same format as the thickness files, so you can extract them using mris_anatomical_stats (providing you have your own annotation). The command will look something like: mris_anatomical_stats -a $SUBJ/label/YOUR_ANNOT -t $SUBJ/surf/?h.pial_lgi -f

Re: [Freesurfer] Question about LGI

Hi Panos, It all depends on what your question is: whether the between-group difference in LGI and surface area is an absolute difference (then don't correct), or whether you want to see if it holds after correction. In any case, by geometric definition, the relationship between surface area,

Re: [Freesurfer] Question about LGI

Hi Panos, Then I would say that it's interesting to understand why the results change depending on the correction. Here is a list of papers that may be relevant, but you'll certainly find many others: http://www.ncbi.nlm.nih.gov/pubmed/8159014 http://pages.jh.edu/~kechen/pnas-brains.pdf

Re: [Freesurfer] LGI error

Hi Alan, You probably don't have the matlab image processing toolbox installed. Let me know if you can't install it easily. Best, Marie On Jul 9, 2014, at 11:51 AM, Alan Francis alandarkene...@gmail.commailto:alandarkene...@gmail.com wrote: Hi Marie FreeSurfers: I am running the LGI

Re: [Freesurfer] localGI problems

to force the removal, it could be an idea. I'll let you know. Ehm... what do you mean by to process the LGI on another computer? Do you think it is a problem linked to the OS? Best, Elisa 2014-07-02 19:17 GMT+02:00 Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch: Hello Elisa

Re: [Freesurfer] localGI problems

Hello Elisa, I've seen this issue that the process gets stuck even if you answer the question. That happened to me and others before, see the following posts: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg07251.html

Re: [Freesurfer] pial layers

Hi Mia, I'm not sure to understand what you mean with pial layers. Recon-all -lgi computes the local gyrification index. Can you please send the full command and full log of the error that you get? Best, Marie On 4 juin 2014, at 19:47, Borzello, Mia

Re: [Freesurfer] pial layers

-all.log (attached)? Thanks so much, m From: freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Marie Schaer [marie.sch

Re: [Freesurfer] Longitudinal recon-all –localGI after error on cross recon-all –localGI and optimal smoothing

Hi Knut, Basically as you reprocessed totally your surfaces, yes it is safer to reprocess the longitudinal stream to make sure that everything is coherent. As for the smoothing, lGI is already inherently very smoothed, so you definitely have to take a lower FWHM than for thickness. When you

Re: [Freesurfer] Longitudinal recon-all –localGI after error on cross recon-all –localGI and optimal smoothing

2013b for localGI? Best regards, Knut J On 05/29/2014 11:05 PM, Marie Schaer wrote: Hi Knut, Basically as you reprocessed totally your surfaces, yes it is safer to reprocess the longitudinal stream to make sure that everything is coherent. As for the smoothing, lGI is already

Re: [Freesurfer] mris_anatomical_stats lgi error

Hi Andreia, Then I would guess that your error comes from the fact that you didn't rerun the autorecon3 at that stage for these 2 subjects. As the randomness flag changes the number of vertices when recreating the surfaces, that explains the error. So for your subjects, just rerun autorecon3

Re: [Freesurfer] mris_anatomical_stats lgi error

Hi Andreia, You probably have lGI values that correspond to earlier versions of your surfaces (I.e. maybe you ran lGI first, then did corrections on the surfaces and reprocessed them, but forgot to recalculate lGI for this new surfaces). If you simply reprocess lGI now, that should solve the

Re: [Freesurfer] Question regarding IGI

these holes? Thank you, Sincerely, Virendra From: Marie Schaer [mailto:marie.sch...@unige.chhttp://unige.ch] Sent: Wednesday, April 30, 2014 7:50 PM To: Virendra Mishra Cc: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu list Subject: Re: Question regarding IGI Hi Virendra

Re: [Freesurfer] Question regarding IGI

for that reply. So, in principle, if I go and find the holes and fill them and make it a continuous surface, then I should be able to compute IGI, right? Thank you for your help and time. Sincerely, Virendra From: Marie Schaer [marie.sch

Re: [Freesurfer] Question regarding IGI

Hi Virendra, Where does this surface come from? You didn't get this one after running the default recon-all, right? Looking at it I noticed a lots of holes and many small unconnected components on the medial aspect. I ran mris_euler_number and got a total of 68 defects, so I'm afraid you'll

Re: [Freesurfer] LGI - Statistical Analysis

Hi Kenza, (I added the freesurfer mailing list in copy, please post there) You have to set the min threshold at 1 when you overlay the lGI, then you should not see any gray regions anymore. Not sure I understood your problem with the statistical analyses, maybe there is simply no significant

Re: [Freesurfer] localgi make_outer_circle

Hi Charnjit, Can you copy / paste the error message? Otherwise I can't help you. Best, Marie On Apr 2, 2014, at 12:54 PM, Charnjit Sidhu c.si...@bham.ac.uk wrote: Hi, Does anyone know how matlab is called in the localgi process. My script fails during the make_outer_circle process, I

Re: [Freesurfer] localgi make_outer_circle

script when matlab is called? Or are we missing something from our script? Or should we split the process into a further script? I have attached the relevant scripts and output. Can you help me. Thanks Charnjit From: Marie Schaer

Re: [Freesurfer] LGI in Qdec

own, I don't think that this is the problem. Any other ideas? Best, Krista On Fri, Feb 28, 2014 at 4:16 PM, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote: Hi Krista, You need to add the following line in your .Qdecrc: MEASURE1 = pial_lgi and save the change. I don't

Re: [Freesurfer] LGI in Qdec

Thanks! Krista On Wed, Feb 26, 2014 at 7:12 PM, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote: Hi Krista, Can you please run: more ~/.Qdecrc and copy paste the output for me? The rm: No match issue in the qcache is not a problem, it's independent from the issue

Re: [Freesurfer] LGI in Qdec

exited without errors. Could this be the problem? If not, does anyone have any ideas? Thanks! Krista On Mon, Feb 24, 2014 at 4:29 PM, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote: Hi Krista, Can you be more specific about what is not coming up? If lGI not listed

Re: [Freesurfer] LGI in Qdec

Hi Krista, Can you be more specific about what is not coming up? If lGI not listed in the menu of qdec, look at the following post: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33427.html Otherwise can you describe more precisely the issue? Best, Marie On Feb 24, 2014,

Re: [Freesurfer] local_gi problem

Hi Krista, Try using the following command: tksurfer BV2 lh inflated -overlay $SUBJECTS_DIR/BV2/surf/lh.pial_lgi -fthresh 1 The error you got is because the overlay needs the full path to the pial_lgi file. Then, not all regions are coloured because the default minimum threshold is 2, and

Re: [Freesurfer] error in local gyrification : error in dsearchn; error in mesh_vertex_nearest; reorganize_verticeslist.....

Hi Guoying, Yes we have a bug with the more recent Matlab versions. You'll find all the details to solve it there: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30506.html Let me know if it doesn't help, Marie On Feb 7, 2014, at 6:54 AM, Wang, Guoying

Re: [Freesurfer] Significant cluster only shows up in the terminal but not on the template brain

Hi Tudor, Seems to me that it could be just a display issue, as you didn't adjust the visualisation threshold (you have min = 2), whereas you run your Monte Carlo with a threshold of 0.05 (i.e. 1.3), and your cluster seem to be just in between. Hope it helps, Marie On Feb 2, 2014, at

Re: [Freesurfer] LGI ERROR: make_roi_paths did not complete successfully!

2014 15:09, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote: Hi Wanda, I'm not sure to understand your problem. Do you get an error because of using matlab 2013? If yes, I'm not sure to understand whether you modified the SearchProjectionOnPial.m function properly. Can you

Re: [Freesurfer] LGI ERROR: make_roi_paths did not complete successfully!

Hi Wanda, I'm not sure to understand your problem. Do you get an error because of using matlab 2013? If yes, I'm not sure to understand whether you modified the SearchProjectionOnPial.m function properly. Can you download the updated function there:

[Freesurfer] transferring annotation from one subject to another

Hi all, I have an annotation for fsaverage that I would like to convert into a subject's space. Up to now, the only way I found to do that was to convert my annotation to all its labels, and then rebuilt the annotation in the subject's space from the labels, using the following 3 steps

Re: [Freesurfer] pial_lgi in QDEC

Sophie, Try to add the line MEASURE1 = pial_lgi in the .Qdecrc in your home folder instead, that should make pial_lgi automatically listed in qdec. Let me know if it doesn't work, Marie On Jan 13, 2014, at 8:11 AM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu

Re: [Freesurfer] LGI computation problem

Hi Wee, We have an issue using lGI with matlab 2013 in the current version. It will be updated in the new version, but in the mean time if you want to use it, it's a very small change that you have to do. See the following post:

Re: [Freesurfer] LGI　error

Hi Kangchen, I also had the same error recently on a unix machine, but I unfortunately did not find the solution and some help would be greatly appreciated. I think that the bug is due to the fact that make_outer_surface.m calls MRIread.m, which calls load_mgh.m and that something gets wrong

Re: [Freesurfer] LGI　error

to load_mgh.m because the temporary filename would be different. However, it is consistent with the temp files used with nifti reading and writing. Does that happen in the lGI stream? doug On 12/06/2013 01:46 PM, Marie Schaer wrote: Hi Kangchen, I also had the same error recently on a unix machine, but I

Re: [Freesurfer] LGI　error

reliably so that you could test it? doug On 12/06/2013 03:02 PM, Marie Schaer wrote: Many thanks Doug for your reply! For me it happened every time the lGI was launched, but none of the other freesurfer commands that I used on this system ever resulted in a similar error

Re: [Freesurfer] localGI Matlabpath

path I ment that the path just did not change. Here is my entire log. Thank you very much for your help. Kind regards Christiane Von: Marie Schaer [mailto:marie.sch...@unige.chhttp://unige.ch] Gesendet: Montag, 18. November 2013 21:03 An: Jockwitz, Christiane Cc: freesurfer

Re: [Freesurfer] localGI Matlabpath

Hi Christiane, What do you mean when you say that you get the old path with getmatlab? In any case, the error seems not related to a matlab path issue. Can you please attach the entire log? Marie On Nov 18, 2013, at 12:03 AM, Jockwitz, Christiane

Re: [Freesurfer] localGI Matlab runtime?

Hi Ryan, Sorry I have no experience with that. But two years ago someone from the mailing list posted the following approach: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19239.html. Maybe they can help you with that, or maybe someone else from the mailing list knows

Re: [Freesurfer] LGI path problem

in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); ERROR: make_roi_paths did not complete successfully! On Wed, Oct 23, 2013 at 4:04 PM, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote: Hi Linn, If you

Re: [Freesurfer] Fwd: LGI path problem

Mar 12 14:18:09 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj exited with ERRORS at Wed Oct 23 08:20:58 BST 2013 Thank you very much for your time and help, Kind Regards,Linn On Tue, Oct 22, 2013 at 10:50 PM, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote

Re: [Freesurfer] Fwd: LGI path problem

Hi Linn, Sorry for the delay in answering. The path has to be set directly in your environment variable (the variable $PATH has to point to the correct version). I need a few more details about what you tried and which OS you are using to be able to help you. If you are using mac, here is an

Re: [Freesurfer] LGI radius

Hi Jon, The fastest way is probably to change the radius value on row 40 in mris_compute_lgi. We originally intended to make an option for setting the radius, but I realize that we forgot it in the end. I'll see if we can change it for the next version, but in the mean time change the value

Re: [Freesurfer] Qdec analysis -- Don't use DOSS with QDEC

Hi Doug, I'm jumping in the discussion because I was a bit scared with your previous email mentioning that this DOSS bug affects all FreeSurfer's versions. Does that also affect statistical analyses computed with mri_glmfit using the command line? Do you have an insight whether the bias

Re: [Freesurfer] Extracting LGI values

literal for float(): ThickAvg Am I doing something wrong? Thanks again, Alan On Tue, Sep 3, 2013 at 5:11 PM, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote: Hi Alan, lGI is different from the folding index. lGI is not yet extracted automatically in the different regions

Re: [Freesurfer] Monte Carlo Simulation in Qdec

Hi Tara, You can try with fwhm=0 as Doug suggested, or 5 if it works. I'm still trying to see whether the level of fwhm could be modified in qdec so that you can input your own level (e.g. 1 or 2, instead of the specified 0-5-10-15-20-25). Nick, Do you know if there is a keyword that can be

Re: [Freesurfer] Extracting LGI values

Hi Alan, lGI is different from the folding index. lGI is not yet extracted automatically in the different regions, because it's more meant to be use at the vertexwise level. But you can easily obtain the lGI values averaged over the Desikan's ROI using the following command:

[Freesurfer] adding smoothing values in qdec's menu

Hi all, I have a quick question related to Qdec. I know that some menus can be changed by modifying .Qdecr. Is there one keyword that will allow me to add different smoothing values to the FWHM menu? Many thanks in advance for your answer, Marie

Re: [Freesurfer] LGI

Hi Jeonghwan, Yes sorry, this is an issue that I recently discovered with Matlab versions starting R2013a (R2013b is also concerned). The bug is related to a change in one variable which for a strange reason is now read as a column vector instead of a row vector. You'll find the patch

[Freesurfer] using two vs one scan(s) for optimal surface reconstruction

Hi all, Small question related to the number of structural runs required for optimal results: I was wondering whether someone tested the assumption that using two scans rather than one improves the segmentation process and the cortical surface reconstruction / thickness estimation? I've not

Re: [Freesurfer] recon-all -localGI results in ERROR:: Too many arguments.

, but none of the missing rh.pial_lgi were created, this time without an obvious error message left behind (see log files of recon-all -localGI attached). Thanks again for your help! Tudor On 17 June 2013 20:46, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote: Hi Tudor, Good

Re: [Freesurfer] recon-all -localGI results in ERROR:: Too many arguments.

very much for your help Marie! Tudor On 14 June 2013 19:53, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote: Hi Tudor, Then the problem is certainly related to the fact that you don't have matlab (the folder /usr/local/freesurfer/matlab is not the matlab distribution, rather

Re: [Freesurfer] recon-all -localGI results in ERROR:: Too many arguments.

Hi Tudor, Yes you will need matlab with the image processing toolbox installed. The issue may be that you are running FreeSurfer in a virtual machine, with matlab not installed there. But, as Doug mentioned, I would assume the algorithms to answer you that it didn't find matlab. So, a few

Re: [Freesurfer] recon-all -localGI results in ERROR:: Too many arguments.

do you make of this? Thanks again! Tudor On 14 June 2013 17:31, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote: Hi Tudor, Yes you will need matlab with the image processing toolbox installed. The issue may be that you are running FreeSurfer in a virtual machine

Re: [Freesurfer] LGI radius on outer surface ?

Hello Gregory, The radius of the circular region is 25 mm by default. If you want you can change it, but I will not advise radii below 20 mm or above 30 mm. Best, Marie On May 13, 2013, at 11:44 AM, Gregory Kirk gk...@wisc.edu wrote: Hello Im preparing an LGI(local gyrification

Re: [Freesurfer] unit of corpus callosum segmentation

: Hi Marie It is mm^3 of I believe a 5 mm thick cc. We don't measure the thickness by default Cheers Bruce On Apr 13, 2013, at 2:18 AM, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote: Hi Bruce, Thanks for your response. My question was indeed: what is the unit of the CC_

[Freesurfer] unit of corpus callosum segmentation

Hi all, I have a quick question related to the corpus callosum segmentation: I read in previous posts that the reference explaining more about the CC subdivision in 5 segments was the one by Rosas et al, Neuroimage 2010. But in this publication, you show thickness of the corpus callosum as

Re: [Freesurfer] LGI

Hi Jon, It looks like the matlab path is not set on your machine. Can you set the $PATH environment variable to include the path to the matlab functions as well? You can try to launch the command getmatlab, if you get the answer that matlab is not installed, it means that the $PATH

Re: [Freesurfer] LGI

://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting - Original Message - From: Marie Schaer marie.sch...@unige.ch To: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Monday, March 18, 2013 1:07:54 PM Subject: Re: [Freesurfer] LGI Hi Jon, It looks like the matlab

Re: [Freesurfer] LGI Path Question

Hi Adam, The place to define matlab is not set in freesurfer, but directly in your environment variables. You have to add the path to your matlab installation directory to the variable $PATH. However, what I am not able to figure out, is why it doesn't work with Matlab 2010. I tested it with

[Freesurfer] rotation applied by mri_convert

Hi everyone, I have a question related to mri_convert (I use FreeSurfer version 5.1). I noticed that when I convert some images without specifying anything about the orientation (mri_convert MY_DICOMS 001.mgz), in a high proportion of the case, mri_convert will identify an orientation matrix

Re: [Freesurfer] local GI calculation Error

Hi Gabriel, It may be the case that because of the surface topology, the lGI fails on one vertex. Most of the time, just recomputing the surface creation solves the problem. Can you try to run recon-all -autorecon2-wm -autorecon3 -randomness -hemi lh -s c_36 and then rerun the lgi computation

Re: [Freesurfer] error measuring LGI

Gabriel, If I am correct, your path (fsmatlab) is pointing to the matlab folder of freesurfer distribution (I.e. Including the matlab scripts) whereas it should point to the matlab installation directory. You can check using the command getmatlab. Let me know, Marie On 16 oct. 2012, at

Re: [Freesurfer] error measuring LGI

command and said that matlab does not exist, I'm guessing this is the problem. Bests, Gabriel El 16/10/12, Marie Schaer marie.sch...@unige.ch escribió: Gabriel, If I am correct, your path (fsmatlab) is pointing to the matlab folder of freesurfer distribution (I.e. Including

Re: [Freesurfer] error measuring LGI

: Marie, I'm working on centOS 4, I'd add the path to the matlab installation folder on my PATH as: setenv MATLABPATH /root/trabajo/matlab2009 setenv PATH ${MATLABPATH}/bin:${PATH} And this is not working still Any ideas? Gabriel El 16/10/12, Marie Schaer marie.sch...@unige.ch

[Freesurfer] mapping label to vol and aseg to vol

Hi FreeSurfer team, I have two small questions related to exporting label or aseg into mgz volumes: 1) I want to save one label into a volume, I used mri_label2vol which works perfectly, but I am getting only a thin label. I saw that I can use the --proj option with mri_label2vol to increase

[Freesurfer] -legacy flag in version 5.1

Hi everyone, Just a quick question: I noticed that the -legacy option of recon-all was removed in version 5.1. Is there any way to keep the manual edits and all the processing from previous versions while reprocessing with 5.1? Thank you very much, Marie

Re: [Freesurfer] gyrification Index of a label

Hi Ritobrato, Nick already answered your query. Just a small add: the gold standard to use local gyrification index is to compute vertex-wise analyses rather than parcel-wise comparisons. Indeed, lGI at each point already quantifies the gyrification in the surrounding region. As a result, the

Re: [Freesurfer] lGI value is aberrantly high

Wayne, You can try to rerun the surface reconstruction (recon-all -autorecon2-wm -randomness, in order to change the number of vertices, and then recon-all -autorecon3) and then rerun the lgi process (recon-all -lgi), this should solve the problem. If not, please let me know. Marie On Jun

Re: [Freesurfer] lGI value is aberrantly high

/Linux recon-all exited with ERRORS at Tue Jun 28 06:20:34 EDT 2011 Do I do the same thing that you recommended? thanks, Alan On Tue, Jun 28, 2011 at 4:53 AM, Marie Schaer marie.sch...@unige.ch wrote: Wayne, You can try to rerun the surface reconstruction (recon-all -autorecon2

[Freesurfer] PhD position in structural imaging of the vulnerability to develop schizophrenia

with a letter of motivation and their detailed marks during their Master (or latest achieved degree) to Dr. Marie Schaer, marie.sch...@unige.ch. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

Re: [Freesurfer] 2 questions on folding index, local gyrification index

Hi Chris, Regarding your question on lGI, I am sure that imclose is one of the required function belonging to the Image Processing Toolbox. I may be wrong but I think that it is the only one. More specifically I don't remember that I used fspecial, where did you see it? (Apart from imclose,

Re: [Freesurfer] LGI failure

Hi Lena, Sorry for the delay in answering, happy Christmas and new year too! Could you please send me the whole error output? Thanks, Marie On Dec 25, 2010, at 10:37 AM, Lena Palaniyappan wrote: Hi Marie/ list Happy Christmas/New Year!! Any idea why this is happening while I try to

Re: [Freesurfer] Mean lGI value extraction

Hi Prapti, Normally you can use aparcstats2table exactly as you would do with thickness, given that the column corresponding to thickness values in the tablefile that you produced with your mris_anatomical_stats are indeed lgi values (i.e. you used mris_anatomical_stats -t pial_lgi -f

Re: [Freesurfer] Mean lGI value extraction

-Original Message- From: Marie Schaer [mailto:marie.sch...@unige.ch] Sent: Wed 11/17/2010 12:39 AM To: Prapti Gautam Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mean lGI value extraction Hi Prapti, Normally you can use aparcstats2table exactly as you would do

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