[Freesurfer] mri_thickness mri_make_surfaces
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 ___ 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.
Re: [Freesurfer] WM Pial Segmentation Errors
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 +, 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, I¹ve been having trouble on a few of our subjects with getting the white matter and pial surface files to ³line up² correctly with the volume files. I¹ve 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 ³good² subject for comparison. I¹ve tried looking through the tutorials online but didn¹t 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 ___ 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] deployed (compiled) MATLAB scripts path manipulation
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'
)
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] excluding labels
Hi all,Would be great is someone can tell me how to exclude user-definedlabels from the analysis.As far as I understand after creating all labels, mris_label2annot with a custom colortable should be used.-Is this correct or is there a more efficient way to exclude labels form analysis?-How can the new annotation file be incorporated with old annotation files to mark what should be excluded/included in the analysis?-Can a similar operation be done directly for labels created in Tkmedit and volumes?Thank you very much in advance!Best,ruthi___ 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] 8 spots remain in the FreeSurfer course
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 ___ 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] FSGD Format Error
Hi all, I have been struggling with my .fsgd file. Its header is the following (a total of 119 subjects): GroupDescriptorFile1 TitlePatients_vs_Controls MeasurementNamethickness ClassPxMale ClassPxFemale ClassConMale ClassConFemale ClassPxMPRAGE ClassPxSPGR ClassConMPRAGE ClassConSPGR ClassMaleMPRAGE ClassMaleSPGR ClassFemaleMPRAGE ClassFemaleSPGR VariablesAge InputFS_1PxFemalePxMPRAGEFemaleMPRAGE51 ..(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! ___ 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] lgi mris_preproc
Hi, In the wiki page on the gyrification index it says that to sample the results to ico, use recon-all -s my_subject_id -qcache -measure pial_lgi If I prefer not to use qudec, can I instead use mris_preproc to do the registration to atlas and concatenate the files and then use mri_surf2sruf to smooth? And then proceed with inferential statistics? Thank you! --- from the wiki: The primary output file is ?h.pial_lgi, which can be viewed as an overlay in tksurfer or freeview: tksurfer my_subject_id lh inflated -overlay lh.pial_lgi To perform a vertex-wise analysis in QDEC of the lgi surface data, first sample the results to the average template subject 'fsaverage': recon-all -s my_subject_id -qcache -measure pial_lgi Do this for each of the subjects in your group -- yours, Lars M. Rimol, PhD Norwegian University of Technology and Science (NTNU) Trondheim, Norway ___ 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.
Re: [Freesurfer] lgi mris_preproc
you should be able to use mris_preproc On 10/9/14 1:08 PM, Lars M. Rimol wrote: Hi, In the wiki page on the gyrification index it says that to sample the results to ico, use recon-all -s my_subject_id -qcache -measure pial_lgi If I prefer not to use qudec, can I instead use mris_preproc to do the registration to atlas and concatenate the files and then use mri_surf2sruf to smooth? And then proceed with inferential statistics? Thank you! --- from the wiki: The primary output file is ?h.pial_lgi, which can be viewed as an overlay in tksurfer or freeview: tksurfer my_subject_id lh inflated -overlay lh.pial_lgi To perform a vertex-wise analysis in QDEC of the lgi surface data, first sample the results to the average template subject 'fsaverage': recon-all -s my_subject_id -qcache -measure pial_lgi Do this for each of the subjects in your group -- yours, Lars M. Rimol, PhD Norwegian University of Technology and Science (NTNU) Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FSGD Format Error
Each subject can only have one class. So, if you have males and females who are conotrols and ADs, then you would have 4 classes, and each subject could only belong to one class On 10/9/14 11:55 AM, Retzepi, Kallirroi wrote: Hi all, I have been struggling with my .fsgd file. Its header is the following (a total of 119 subjects): GroupDescriptorFile1 TitlePatients_vs_Controls MeasurementNamethickness Class PxMale Class PxFemale ClassConMale ClassConFemale ClassPxMPRAGE ClassPxSPGR ClassConMPRAGE ClassConSPGR ClassMaleMPRAGE ClassMaleSPGR ClassFemaleMPRAGE ClassFemaleSPGR VariablesAge InputFS_1PxFemalePxMPRAGEFemaleMPRAGE51 ..(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! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] excluding labels
What analysis? On 10/9/14 11:35 AM, Adam, Ruth wrote: Hi all, Would be great is someone can tell me how to exclude user-defined labels from the analysis. As far as I understand after creating all labels, mris_label2annot with a custom colortable should be used. -Is this correct or is there a more efficient way to exclude labels form analysis? -How can the new annotation file be incorporated with old annotation files to mark what should be excluded/included in the analysis? -Can a similar operation be done directly for labels created in Tkmedit and volumes? Thank you very much in advance! Best, ruthi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Study design for qdec or command line group analysis
Hi all, Sorry for the follow up but hope someone can clarify following doubts. Thanks, Sneha From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sneha Pandya [snp2...@med.cornell.edu] Sent: Tuesday, October 07, 2014 1:06 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Study design for qdec or command line group analysis Dear freesurfers, I have a study in which we want to perform group analysis to find the effect of age on cortical thickness between patients and controls. We have 11 patients with age group from 45-75 years and the mean of 53. We shall age match our controls with respect to similar age range and mean. However our patient scans are from both 1.5T and 3.0T scanner, hence I have few questions about designing our study. A) Can we treat certain discrete factors as continuous variables, like gender (male with value 1 and female with value 2), and scanner (1.5T with value 1 and 3.0T with value 2) to make group analysis qdec-able in case of 3 discrete factors? I tried to look into mailing archive to figure out the answer, but so far found confounding answers. B) If what asked above is possible can you please suggest which design I should opt for? Design 1) Three discrete factors, each with 2 levels: (i) gender (male and female) (ii) groups (healthy and patients) (iii) scanner (1.5T and 3.0T), Continuous variable: (i) age OR Design 2) Two discrete factors, each with 2 levels (i) gender (male and female) (ii) groups (healthy and patients) Continuous variables: (i) age (ii) scanner (1.5T as 1, and 3.0T as 0) From literature we are not expecting any effect of gender and scanner on change of cortical thickness with age between groups, however I guess we need to control for it right? Should I implement design 1 with mri_glmfit command line, as it has 3 discrete factors or design 2 in qdec? B) We are expecting some change in cortical thickness with age between groups. Hence we shall be using DODS model to perform the analysis. In this case I should demean my ages right (subtract grand mean of age from combined healthy and patient groups and subtract from every individual age)? Thanks, Sneha ___ 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.
Re: [Freesurfer] Surface Viewer Issue.
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 + 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 +, 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
