Hi Greg, Is this simply an image viewing problem or does the data actually need to be re-processed? (I'm working with ~500 subjects, so I figured I would check before taxing the servers I had access to).
Thanks much! Best, Jamie. On Thu, Oct 9, 2014 at 12:00 PM, <freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Surface Viewer Issue. (Gregory Kirk) > 2. Re: Mismatched dimensions with T1 and Flair inputs {Disarmed} > (Vilde) > 3. Re: v5.1 control point mri_ca_normalize bug (Marx, Gabe) > 4. Re: v5.1 control point mri_ca_normalize bug (Bruce Fischl) > 5. Re: rawfunc2surf-sess with a limited set of surface files > (Douglas N Greve) > 6. functional correlation (Brian Donley) > 7. Re: rawfunc2surf-sess with a limited set of surface files > (Reza Rajimehr) > 8. mri_thickness & mri_make_surfaces (Seung-Goo KIM) > 9. Re: WM & Pial Segmentation Errors (Varjabedian, Ani) > 10. "deployed" (compiled) MATLAB scripts path manipulation > (sle...@nmr.mgh.harvard.edu) > 11. 8 spots remain in the FreeSurfer course (Allison Stevens) > 12. excluding labels (Adam, Ruth) > 13. FSGD Format Error (Retzepi, Kallirroi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 08 Oct 2014 14:47:27 -0500 > From: Gregory Kirk <gk...@wisc.edu> > Subject: Re: [Freesurfer] Surface Viewer Issue. > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <76a0cbb215b316.54354...@wiscmail.wisc.edu> > Content-Type: text/plain; CHARSET=US-ASCII > > i saw this problem on one redhat installation, not on any others, seems > something with the X library orientation > information and openGL > > greg > > On 10/08/14, Jamie Hanson wrote: > > Hi Freesurfer List, > > > > > > I had a (hopefully quick) question about surface viewers and data > orientation in tksurfer v. freeview. > > > > > > I processed all my data in freesurfer v5.3.0 (on a linux cluster) and > noticed something odd when I viewed surfaces. For tksurfer, the surfaces > were upside down when I opened them (see attached pic: tksurfer.png); for > freeview, the data looked fine (see attached pic: freeview.png). > > > > > > I believe the orientation of the images is correct (judging by the > freeview axes), but wondered if this was something others had run into? I > uploaded an example subject to the Martinos Center FileDrop (link: > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=9491zcnivqw). > > > > > > Any thoughts are greatly appreciated! Thanks much! > > > > > > Best, > > Jamie. > > > > > > > > -- > > Jamie L. Hanson > > Postdoctoral Fellow, Carolina Consortium on Human Development > > Duke University > > 417 Chapel Drive > > Duke West Campus > > Sociology-Psychology Building, Room 07A > > Durham, NC 27710 > > Email: jamielarshan...@gmail.com > > Website: http://jamiehanson.org/ > > > ------------------------------ > > Message: 2 > Date: Wed, 8 Oct 2014 22:01:06 +0200 > From: Vilde <vildesk...@hotmail.com> > Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair > inputs {Disarmed} > To: <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <dub122-w3321c71b2bec2fa5d6be4cd2...@phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > I will try that. > > Have a good day! > > Date: Wed, 8 Oct 2014 14:07:38 -0400 > From: fis...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs > > you would have to first run recon-all -all on the T1 > On Wed, 8 Oct 2014, > Vilde wrote: > > > Thank you Bruce! > > > > If I understand you correctly, would the command be > > > > Recon-all -s subj_name -FLAIRpial.nii ? > > > > Or would I first have to do recon-all with only T1 as input and then do > > another command after it has finished running? And in that case, what > would > > that command be? > > > > Best, > > Vilde > > > > Date: Wed, 8 Oct 2014 11:56:51 -0400 > > From: fis...@nmr.mgh.harvard.edu > > To: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs > > > > Hi Vilde > > > > no, you can't give recon-all a flair directly, it needs a T1 do do the > > recon on. You use the flair at the end to do a post-hoc deformation using > > -flairpial I believe > > > > cheers > > Bruce > > > > > > On Wed, 8 Oct 2014, Vilde wrote: > > > > > Dear mailing list, > > > I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, > for > > > pial surface refinement. This results in an error message saying the > > > dimensions are mismatched. (The third dimension of the T1 and Flair are > > > different by one slice. ) I do not, however, have a problem running > > > recon-all with only one T1 input. I am using Freesurfer v 5.1 . > > > > > > I read in the release notes that in version 5.2 you can use the flag > -FLAI > > R > > > when you are using a flair image as input. I suppose this will not run > in > > an > > > earlier version? > > > Would it be correct to use the following command : > > > > > > recon-all -s [subject] -i T1.nii -i flair.nii -all > > > > > > Kind regards, > > > Vilde > > > > > > > > > > > > > _______________________________________________ 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. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141008/7d22519d/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Wed, 8 Oct 2014 21:02:34 +0000 > From: "Marx, Gabe" <gabe.m...@ucsf.edu> > Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <efc972bc4d7d0340a51a7b3a4dd397ccc68...@ex06.net.ucsf.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Bruce, > > I appreciate the response! > > I am sorry, I am a bit confused. The release notes state: > > "An option is to disable the running of mri_ca_normalize when re-running > the -autorecon2 or -autorecon2-cp stage after adding control points by > adding the flag -nocanorm to the end of recon-all. We will continue to > investigate a more automated solution to detection of this problem. The > more permanent workaround for v5.1 users is to edit their recon-all script > making the following change, which will disable usage of control points > with ca_norm: > > # find these lines: > set cmd = (mri_ca_normalize) > if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) > > # and comment-out the second line like this: > set cmd = (mri_ca_normalize) > #if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) > > # then re-run your subjects with the flags: -autorecon2 -autorecon3 > -clean-aseg" > > Are you saying the -nocanorm flag will result in inaccurate data? > > Thanks! > Gabe > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Wednesday, October 08, 2014 8:12 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug > > Hi Gabe > > this wasn't really a bug per-se, just induced some behavior that people > didn't like. You can't skip the mri_ca_normalize step or the aseg won't be > accurate. The aseg patch I believe just starts autorecon2-cp after the aseg > hs been created, but Nick or Zeke can correct me if I'm wrong. > > cheers > Bruce > > > > On Mon, 6 Oct 2014, Marx, Gabe wrote: > > > > > Hello Freesurfer experts, > > > > ? > > > > I had a question regarding the v5.1 control point mri_ca_normalize > > bug. I read the release notes and know that this bug can be worked > > around by adding the ?nocanorm flag to my recon-all however I have > > become worried about the ramifications of skipping mri_ca_normalize in > my pipeline. > > Would someone be able to give me a better description as to what > > mri_ca_normalize is doing and what I am sacrificing by taking it out > > of my pipeline? Furthermore, in regards to the patch for the recon-all > > script to fix this bug, what is the patch doing exactly? ?If I had > > some data in which I used the ?nocanorm flag and other data in which I > > used the patch would I still be able to make valid analysis if I merged > them? > > Would there be significant inconsistencies? > > > > ? > > > > Thanks! > > > > ? > > > > Best, > > > > Gabe > > > > > > > > > > ------------------------------ > > Message: 4 > Date: Wed, 8 Oct 2014 17:05:41 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Cc: Nick Schmansky <ni...@nmr.mgh.harvard.edu> > Message-ID: <alpine.lrh.2.03.1410081705140.27...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > I don't think you want to run with -nocanorm. Just commenting out the > addition of the -f $ControlPointsFile should be sufficient. Right Nick? > On > Wed, 8 Oct 2014, Marx, Gabe wrote: > > > Hi Bruce, > > > > I appreciate the response! > > > > I am sorry, I am a bit confused. The release notes state: > > > > "An option is to disable the running of mri_ca_normalize when re-running > the -autorecon2 or -autorecon2-cp stage after adding control points by > adding the flag -nocanorm to the end of recon-all. We will continue to > investigate a more automated solution to detection of this problem. The > more permanent workaround for v5.1 users is to edit their recon-all script > making the following change, which will disable usage of control points > with ca_norm: > > > > # find these lines: > > set cmd = (mri_ca_normalize) > > if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) > > > > # and comment-out the second line like this: > > set cmd = (mri_ca_normalize) > > #if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) > > > > # then re-run your subjects with the flags: -autorecon2 -autorecon3 > -clean-aseg" > > > > Are you saying the -nocanorm flag will result in inaccurate data? > > > > Thanks! > > Gabe > > > > -----Original Message----- > > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > > Sent: Wednesday, October 08, 2014 8:12 AM > > To: Freesurfer support list > > Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug > > > > Hi Gabe > > > > this wasn't really a bug per-se, just induced some behavior that people > didn't like. You can't skip the mri_ca_normalize step or the aseg won't be > accurate. The aseg patch I believe just starts autorecon2-cp after the aseg > hs been created, but Nick or Zeke can correct me if I'm wrong. > > > > cheers > > Bruce > > > > > > > > On Mon, 6 Oct 2014, Marx, Gabe wrote: > > > >> > >> Hello Freesurfer experts, > >> > >> ? > >> > >> I had a question regarding the v5.1 control point mri_ca_normalize > >> bug. I read the release notes and know that this bug can be worked > >> around by adding the ?nocanorm flag to my recon-all however I have > >> become worried about the ramifications of skipping mri_ca_normalize in > my pipeline. > >> Would someone be able to give me a better description as to what > >> mri_ca_normalize is doing and what I am sacrificing by taking it out > >> of my pipeline? Furthermore, in regards to the patch for the recon-all > >> script to fix this bug, what is the patch doing exactly? ?If I had > >> some data in which I used the ?nocanorm flag and other data in which I > >> used the patch would I still be able to make valid analysis if I merged > them? > >> Would there be significant inconsistencies? > >> > >> ? > >> > >> Thanks! > >> > >> ? > >> > >> Best, > >> > >> Gabe > >> > >> > >> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > ------------------------------ > > Message: 5 > Date: Wed, 08 Oct 2014 17:38:16 -0400 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] rawfunc2surf-sess with a limited set of > surface files > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <5435aec8.3020...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Try it without -i fmc > > > On 10/08/2014 04:38 AM, Reza Rajimehr wrote: > > One more question: > > > > I tried to run: > > > > rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg > > iter05.sphere.reg -fwhm 2 -per-session > > > > And I got this: > > > > ERROR: experts key needed (-expkey) > > > > Not sure what this flag is. > > > > Reza > > _______________________________________________ > > 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/ > > > > ------------------------------ > > Message: 6 > Date: Wed, 8 Oct 2014 16:48:11 -0500 > From: Brian Donley <brian.don...@gmail.com> > Subject: [Freesurfer] functional correlation > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <CAJO=T5tRjhKMPMJh_PuHKDBv= > f0lagpv69so58kyenmcium...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello Freesurfers > > A bit new to the program, so I hope the following makes sense. We would > like to do a bottom-up vertex-by-vertex analysis to see where functional > activation correlates with thickness. We've done our functional analyses > through SPM and can get those maps into tksurfer. Most of the tutorials and > information I see has to do with, for example, defining a ROI based on > functional data and extracting the thickness measures "under" that ROI. But > this would be a little different > > Does this make sense, and is this doable in freesurfer? If so, could > someone point me to the relevant tutorial or commands? > > I appreciate your help > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141008/9ecbc2cf/attachment-0001.html > > ------------------------------ > > Message: 7 > Date: Thu, 9 Oct 2014 00:12:04 -0400 (EDT) > From: "Reza Rajimehr" <r...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] rawfunc2surf-sess with a limited set of > surface files > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <42178.18.93.15.69.1412827924.squir...@mail.nmr.mgh.harvard.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Hi Doug, > > Removing -i fmc did not help, and I still get the same error. > > By looking at the rawfunc2surf-sess script, it looks like specifying an > argument for -surfreg makes ExpKeyNeeded = 1. Can I just specify something > for -expkey? Is this something that is used only in the name of log file? > > Thanks, > Reza > > > Try it without -i fmc > > > On 10/08/2014 04:38 AM, Reza Rajimehr wrote: > > One more question: > > > > I tried to run: > > > > rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg > > iter05.sphere.reg -fwhm 2 -per-session > > > > And I got this: > > > > ERROR: experts key needed (-expkey) > > > > Not sure what this flag is. > > > > Reza > > > ------------------------------ > > Message: 8 > Date: Thu, 9 Oct 2014 12:42:07 +0200 > From: Seung-Goo KIM <sol...@gmail.com> > Subject: [Freesurfer] mri_thickness & mri_make_surfaces > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <4e85c9bd-03cd-4781-a989-432d9eaf7...@gmail.com> > Content-Type: text/plain; charset="windows-1252" > > Hi all, > > I?m trying to compute cortical thickness using mris_thickness (stable 5), > but getting slightly different results from the recon-all 5.1.0-amd64-2.13 > (mri_make_surfaces, stable 5). > > Hinted from an old thread: > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05994.html, > I set the switch ?-N 20", but it returns different values: 50% of vertices > have identical values with the cross-correlation of about 0.98 and RMS of > 0.08 mm, which is of course very high, but a bit odd while I was expecting > nearly identical results. When I checked the scatter plots, the > mris_thickness returns a bit smaller values for many vertices than the > standard result. Is this somewhat expected difference between > mri_make_surfaces and mris_thickness? > > Also I found that mri_thickness reads ??h.gray?, not ??h.pial?. As I > assumed that it reads ??h.pial? and ??h.white? to compute thickness, so I > just linked ??h.pial? to ??h.gray?. Is this assumed input for > mris_thickness? > > > Best regards, > -- > Seung-Goo KIM > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141009/fdd67cc0/attachment-0001.html > > ------------------------------ > > Message: 9 > Date: Thu, 9 Oct 2014 14:01:55 +0000 > From: "Varjabedian, Ani" <avarjabed...@mgh.harvard.edu> > Subject: Re: [Freesurfer] WM & Pial Segmentation Errors > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <1412863314.22885.45.ca...@sangwoo.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Michael, > > I took a look at your data and it seems that you paired a T2 image with > a T1 image when you submitted to recon all. Recon-all will try to > average these together, and since they have such different contrasts, > you will end up with a poor template for surfaces later on. > > Try running recon-all again without the T2 and see if that helps. > > > -Ani > > > On Wed, 2014-10-08 at 17:21 +0000, Smith, Michael wrote: > > Ah, sorry for some reason it just wasn?t clicking before. I was able to > > upload a dataset. Thanks! > > > > On 10/8/14, 10:59 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: > > > > >Hi Michael > > > > > >you need to follow the directions on this page: > > > > > >http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange > > > > > >in particular, make sure you change directories before trying to put > > > > > >cheers > > >Bruce > > > > > >On Wed, > > >8 Oct 2014, > > >Smith, > > >Michael wrote: > > > > > >> See attached > > >> > > >> On 10/8/14, 10:46 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > wrote: > > >> > > >>> can you send us the details of your ftp command? > > >>> On Wed, 8 Oct 2014, Smith, > > >>> Michael wrote: > > >>> > > >>>> Hi Bruce, > > >>>> > > >>>> Do I not have permission to transfer files to the remote machine? I > > >>>>can > > >>>> login fine as an anonymous user but when I attempt to use the put > > >>>> command > > >>>> it says it could not create the file. > > >>>> > > >>>> On 10/7/14, 7:33 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > > >>>>wrote: > > >>>> > > >>>>> Hi Michael > > >>>>> > > >>>>> sure, the T2 can help if you have it (although you'll need to > > >>>>>download > > >>>>> some > > >>>>> updated binaries), but it is impossible to tell from these images > > >>>>>what > > >>>>> is > > >>>>> going on. Looks either the intensity normalization, mri_segment or > > >>>>> mris_make_surfaces failed. You can try the expert options for each > > >>>>>one > > >>>>> to > > >>>>> prespecify the range of allowable intensities for gray and white > > >>>>> matter. > > >>>>> If > > >>>>> you upload the subject to our ftp site (the whole subject directory > > >>>>> tarred > > >>>>> and gzipped) we will take a look > > >>>>> > > >>>>> cheers > > >>>>> Bruce > > >>>>> > > >>>>> On Mon, 6 Oct 2014, Smith, Michael wrote: > > >>>>> > > >>>>>> Hi, > > >>>>>> > > >>>>>> I?ve been having trouble on a few of our subjects with getting the > > >>>>>> white > > >>>>>> matter and pial surface files to ?line up? correctly with the > volume > > >>>>>> files. > > >>>>>> I?ve attached a screenshot of what is happening: the pial surface > > >>>>>>is > > >>>>>> in red > > >>>>>> and the white matter surface file is in yellow. I have also > attached > > >>>>>> an > > >>>>>> example of a ?good? subject for comparison. > > >>>>>> > > >>>>>> I?ve tried looking through the tutorials online but didn?t see > > >>>>>> anything > > >>>>>> that > > >>>>>> was really related to my issue and I was wondering what the best > way > > >>>>>> to > > >>>>>> correct this. We have T2 weighted images for several subjects is > > >>>>>>well > > >>>>>> if > > >>>>>> that helps. Not sure if Freesurfer can use T2 images instead of > T1 > > >>>>>>in > > >>>>>> the > > >>>>>> ?reconall script but I thought I would mention it. Thank you very > > >>>>>> much > > >>>>>> in > > >>>>>> advance! > > >>>>>> > > >>>>>> Best, > > >>>>>> > > >>>>>> Michael S. > > >>>>>> > > >>>> > > >>>> > > >>>> > > >>>> _______________________________________________ > > >>>> Freesurfer mailing list > > >>>> Freesurfer@nmr.mgh.harvard.edu > > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>>> > > >>>> > > >> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ------------------------------ > > Message: 10 > Date: Thu, 9 Oct 2014 11:08:10 -0400 (EDT) > From: sle...@nmr.mgh.harvard.edu > Subject: [Freesurfer] "deployed" (compiled) MATLAB scripts path > manipulation > To: freesurfer@nmr.mgh.harvard.edu > Cc: martinos-t...@yahoogroups.com > Message-ID: > <57088.172.21.16.53.1412867290.squir...@mail.nmr.mgh.harvard.edu> > Content-Type: text/plain;charset=iso-8859-1 > > I have been following the directions on this site to "deploy" (compile) my > MATLAB script so as to be able to run it on launchpad without worrying > about MATLAB licenses. > > https://nmr.mgh.harvard.edu/martinos/itgroup/deploytool.html > > They say that the deployed script cannot do path manipulations such as > addpath() or path(path,xxx), so the script should use isdeployed to make > sure that such path commands are only executed if isdeployed == 0. > > > % Only add path if not deployed > if isdeployed==0; > addpath ~nummenma/matlab/work/connectome/HCP_preproc_tools; > end > > but then I need to add the path back in again so it can access the > functions on that path. In the deploytool GUI I click Settings (the little > gear icon), and in the upper window "Additional Parameters passed to MCC:" > I inserted > > ======[ Additional Parameters passed to MCC: ]====== > -I ~nummenma/matlab/work/connectome/HCP_preproc_tools > mris_gradient_nonlin__unwarp_volume__batchmode_HCPS.m > ==================================================== > > (A web site I found said you need a path to the m-file itself, not just to > the directory that contains it, and you separate the path and file) > > Then I found I had to circumvent more path(path,xxx) commands in my > startup.m file too > > ======[ startup.m ]====== > % If script is not deployed add paths > if isdeployed==0; > %------------ FreeSurfer -----------------------------% > fshome = getenv('FREESURFER_HOME'); > fsmatlab = sprintf('%s/matlab',fshome); > if (exist(fsmatlab) == 7) > path(path,fsmatlab); > end > clear fshome fsmatlab; > %-----------------------------------------------------% > > %------------ FreeSurfer FAST ------------------------% > fsfasthome = getenv('FSFAST_HOME'); > fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); > if (exist(fsfasttoolbox) == 7) > path(path,fsfasttoolbox); > end > clear fsfasthome fsfasttoolbox; > %-----------------------------------------------------% > end > ========================= > > Now at least it compiles without error. But when I run it I get this: > > Set up FreeSurfer environment > -------- freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 > FSFAST_HOME /usr/local/freesurfer/stable5_3_0/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /space/ficus/4/users/SNEF_subjects > MNI_DIR /usr/local/freesurfer/stable5_3_0/mni > FSL_DIR /usr/pubsw/packages/fsl/current > ./run_unwarpone.sh > /cluster/matlab/8.2 > > /space/ficus/4/users/SLOTS_sessions_Step/SLOTS010/aahscout/001/001.mgz > > /space/ficus/4/users/SLOTS_sessions_unwarp/SLOTS010/aahscout/001/001.mgz > > /space/ficus/4/users/SLOTS_sessions_Step/SLOTS010/unwarpscout001.log > ------------------------------------------ > Setting up environment variables > --- > LD_LIBRARY_PATH is > > .:/cluster/matlab/8.2/runtime/glnxa64:/cluster/matlab/8.2/bin/glnxa64:/cluster/matlab/8.2/sys/os/glnxa64 > The file > '/usr/local/freesurfer/stable5_3_0/matlab/load_nifti.m' > is not in the application's expanded CTF archive at > '/homes/6/slehar/.mcrCache8.2/unwarp2'. > This is typically caused by calls to ADDPATH in your startup.m or > matlabrc.m files. Please see the compiler documentation and use the > ISDEPLOYED function to ensure ADDPATH commands are not executed by > deployed applications. > An error occurred while trying to determine whether "load_nifti" is a > function name. > > MATLAB:err_while_looking_up_function > Error:An error occurred while trying to determine whether "load_nifti" is > a function name. > Error:Error in mclFreeStackTrace. > > Any idea what the problem is now? load_nifti is presumably a FreeSurfer > function -- do I now have a problem with my paths to FreeSurfer? I > searched my script code and found no explicit call to "load_nifti", I > presume that is called deep inside some other function. Should I add the > FreeSurfer paths also through the deploytool GUI and not call "nmrenv"? > > (from my .cshrc file... > alias nmrenv 'source /usr/local/freesurfer/nmr-stable53-env' > ) > > > > ------------------------------ > > Message: 11 > Date: Thu, 9 Oct 2014 11:27:07 -0400 (EDT) > From: Allison Stevens <astev...@nmr.mgh.harvard.edu> > Subject: [Freesurfer] 8 spots remain in the FreeSurfer course > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <alpine.lrh.2.03.1410091122430.43...@nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII > > Hello everyone, > We have 8 spots remaining in our upcoming FreeSurfer course happening on > October 27-29. We will accept late registrations up to the course date; > however, since the payment deadline has passed, payment is due immediately > upon registration. > > Details on the course and a link to the registration page can be found > here: > https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription > > Note: This course is the only one where we are currently able to accept > credit card. This likely won't be an option for future courses. > Allison > > > > ------------------------------ > > Message: 12 > Date: Thu, 9 Oct 2014 17:35:52 +0200 > From: "Adam, Ruth" <ruth.a...@med.uni-muenchen.de> > Subject: [Freesurfer] excluding labels > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <4e8bff03-4a73-4634-a54f-c3759cdf5...@med.uni-muenchen.de> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141009/18592f2b/attachment-0001.html > > ------------------------------ > > Message: 13 > Date: Thu, 9 Oct 2014 15:55:35 +0000 > From: "Retzepi, Kallirroi" <kretz...@mgh.harvard.edu> > Subject: [Freesurfer] FSGD Format Error > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <63e2c9a6-fd10-4ee9-a13b-c1d731c6c...@mgh.harvard.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi all, > I have been struggling with my .fsgd file. Its header is the following (a > total of 119 subjects): > > GroupDescriptorFile 1 > Title Patients_vs_Controls > MeasurementName thickness > Class PxMale > Class PxFemale > Class ConMale > Class ConFemale > Class PxMPRAGE > Class PxSPGR > Class ConMPRAGE > Class ConSPGR > Class MaleMPRAGE > Class MaleSPGR > Class FemaleMPRAGE > Class FemaleSPGR > Variables Age > Input FS_1 PxFemale PxMPRAGE FemaleMPRAGE 51 > ..............(rest of subjects) > > > I think something is up with my Class declaration, since the error message > I get is the following: > > ERROR: gdfReadV1: Input line 1, subjid = FS_1 > Found 3 variables, expected. 1 > FSGDF Format Error: file = /group_stats/Px_vs_Con_A.fsgd, tag=Input > > > > Any help would be greatly appreciated!! > > Thank you! > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141009/92cd5c45/attachment-0001.html > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 128, Issue 11 > ******************************************* >
_______________________________________________ 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.
