[Freesurfer] Apply ROI Label from first time point to longitudinal template
Hi All, I have created two ROIs from first time point Qdec group comparison. I need to use this ROI labels to extract the thickness from tp1 and tp2 registered to base (template) subjects(from longitudinal pipeline). Would you please let me how can I convert the label from 1st time point space to longitudinal template space? Best regards, Amirhossein Manzouri ___ 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] hippocampal subfields
Hi Erik,
30 mins for a subject sounds correct. If the text files with the volumes are
there, and the segmentations look plausible, then everything should be fine.
One more thing: it the outputs are in specific directories, please note that we
changed the naming convention and structure of the output last week - sorry
about that! We believe that the changes made the module easier to use. Please
see the updated instructions here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Erik O'Hanlon erikohan...@rcsi.ie
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, May 27, 2015 10:17:51 AM
Subject: Re: [Freesurfer] hippocampal subfields
Hi Eugenio,
I managed to get the subfield code process to run, my cluster wasn't using all
the allotted RAM for the job, thank you for all the input. Can I ask how long
it typically takes as it appears to have completed in about 30mins and gave me
the left and right dirs with the volume txts etc. Just wanted to be sure before
I kick it off on the complete data set.
Thanks again for all the help.
Cheers
Ertik
Erik O'Hanlon
Postdoctoral researcher
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
[e.igles...@bcbl.eu]
Sent: 26 May 2015 11:25
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Hi again,
The software requires approximately 10GB of RAM
Cheers
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Erik O'Hanlon erikohan...@rcsi.ie
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Tue, 26 May 2015 12:16:00 +0200 (CEST)
Subject: Re: [Freesurfer] hippocampal subfields
html
head
style!-- .EmailQuote { margin-left: 1pt; padding-left: 4pt; border-left:
#80 2px solid; } --/style
/head
body
font size=2span style=font-size:10pt;
div class=PlainTextHi Eugenio,br
br
I#39;m trying to run in on a cluster and I think I have eight cores assigned
with 2GB per core. I#39;m not sure if the process is parallelised though so it
could be the case that I have the job running on one of the possible core and
only using 2GB of RAM. I can
ask the cluster support team to check but is it possible to run the job across
the 8 cores and thus grab the 16GB of RAM or will the code only use the
onenbsp; core and I will have to get the RAM assigned to it to be
increased.br
br
Any guidance much appreciated and maybe if you could outline a typical system
requirement/setup to run a job. I have 200 subjects so your advice would
super.br
br
Thanks againbr
br
Cheersbr
br
Erikbr
br
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
[e.igles...@bcbl.eu]br
Sent: 26 May 2015 10:33br
To: Freesurfer support listbr
Subject: Re: [Freesurfer] hippocampal subfieldsbr
br
Hi Erik,br
I guess your process was killed by the kernel. Maybe you ran out of RAM memory?
How much RAM do you have?br
Cheers,br
/Eugeniobr
br
Juan Eugenio Iglesiasbr
Postdoctoral researcher BCBLbr
a href= http://www.jeiglesias.com
target=_blankwww.jeiglesias.com/abr
a href= http://www.bcbl.eu target=_blankwww.bcbl.eu/abr
br
Legal disclaimer/Aviso legal/Lege-oharra: a href=
http://www.bcbl.eu/legal-disclaimer target=_blank
www.bcbl.eu/legal-disclaimer/abr
br
br
- Original Message -br
From: quot;Erik O#39;Hanlonquot; lt;erikohan...@rcsi.iegt;br
To: quot;Freesurfer support listquot;
lt;freesurfer@nmr.mgh.harvard.edugt;br
Sent: Monday, May 25, 2015 6:53:54 PMbr
Subject: Re: [Freesurfer] hippocampal subfieldsbr
br
br
br
Hi FS Experts,br
br
I#39;m trying the v6 hippocampal subfield code on a subject processed with
5.3.0 and I encountered the following error in the log filebr
br
Making Unknown map to reduced label 13br
Computing hyperparameters for estimation of Gaussian parametersbr
Estimating typical intensities of alveusbr
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
line 43: 2675 Killed
quot;${exe_dir}quot;/segmentSubjectT1_autoEstimateAlveusML $argsbr
~br
br
It appears that the process finished prematurely and didn#39;t write out
anything in the mri/ dir.br
br
Any pointers how to resolve ? Any help greatly appreciatedbr
[Freesurfer] Longitudinal study... analyze of results....
Hi: I want to do a longitudinal study between two time points of a patient... I want to compare the volume of the hypocampii, white matter, etc... I did the computation of both time points, I created the base image, and the long ones... How can I analyze the aseg.stats files in each long folder ?... Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] differences in subcortical volumes from version 5.1 to 5.3
Hi Maia that's surprising and a bit worrisome. It's been a while so I don't remember the details of the differences between 5.1 and 5.3. Did you have to edit the aseg in 5.1? cheers Bruce On Wed, 27 May 2015, Maia Pujara wrote: Hi, We ran our subjects through version 5.1, did a thorough quality check and troubleshoot the data, and then re-ran our subjects through version 5.3 to verify that our findings were consistent between versions. We're running into an issue where we are not able to replicate our subcortical findings from version 5.1 to 5.3. We did not do a similar quality check and troubleshooting process for the 5.3 data, but did not think that would affect the estimation of the subcortical segmentations. Are there any reasons why these subcortical values would be different between both versions? Thanks, Maia ___ 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] error mni152 reg
download this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg and copy it to $FREESURFER_HOME/bin doug On 05/26/2015 01:40 PM, Park, Jung Mi wrote: Hello Freesurfer *mni152reg --s 0201JB-anat* *= *mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.31253': Permission denied. Thus I put this command following the way of searching freesurfer mail support. chmod ugo+w /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.31253 chmod: cannot access `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.31253': No such file or directory I am using freesurver 5.3 and FDL 5. 0.7. Please let me know what should I do. Thank you. Linux gencess 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux fslregister --mov /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz --s 0201JB-anat --reg /autofs/cluster/catanagp/users/jumi/subjects/AD/0201JB/0201JB-anat/mri/transforms/reg.mni152.2mm.dat --dof 12 mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.31253': Permission denied ___ 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.
Re: [Freesurfer] Stats file question
Can you list the 3 stats files you are talking about? I can't quite follow from below doug On 05/26/2015 02:21 PM, zal...@u.washington.edu wrote: Hello Freesurfer team, When generating the .stats files for grey matter volumetric data, this information appears in multiple places and I'm not sure which data I should be using for my final results. There appears to be cortical information generated in both the .stats file based off the DKT atlas and the l/rh.aparc.stats file. The information in these files is quite different from one another. Using the FreeSurferColorLUT.txt (as listed in the recon-all dev table) instead of WMParcStatsLUT.txt (which is used when running recon-all) in generating the mri_segstats wmparc.stats file also produces cortical volumetric data. This third set of data differs significantly from the DKT Atlas, and differs less-so from the cortical volumes produced in the aparc.stats file. Which of the .stats files containing grey matter volume data is most accurate? Best, Kody J. Zalewski ___ 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.
Re: [Freesurfer] FW: correcting for brain size
Hi Gabriella, sorry for the delay On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote: HI FS experts, I haven’t heard back and am still wrestling with these questions. Any takers? I’d really appreciate any thoughts at all if possible. Thanks, Gabriella *From:*Hirsch, Gabriella *Sent:* Wednesday, May 20, 2015 3:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I’m hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1.So far, I’ve been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to “mean center” the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? It may or may not be a problem depending on what you are doing. I prefer to divide the glm input value by the ICV, but some like to use as a regressor. If you want to do it that way, then you'll have to demean, or you might try to just scale all ICVs to bring them into a range similar to that of the input value. 2.I’ve found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating – is there any way around this issue? Saying that it crashes is not too informative. Can you give more info? Eg, an error message? 3.If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what’s the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I’m executing this correctly. You can scale the input or scale the ICV as I mention above. You can also run it as a DOSS (different offset, same slope) doug I’d really appreciate any help on this. Thank you! Gabriella ___ 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.
Re: [Freesurfer] Fwd: recon-all issue
don't know. Can you send the recon-all.log file? doug On 05/25/2015 07:13 PM, Anvi K Vora wrote: Hi Doug, That file does not exist, because none of the surf files got created from this pipeline. So there was an error before that? The mri files got created (partially) and what's there looks good. Missing are: aseg.mgz, aparc.a2009s+aseg.mgz, aparc+aseg.mgz, aseg.auto.noCCseg.mgz, aseg.auto.mgz, brain.mgz, brain.finalsurfs.mgz, lh.ribbon.mgz, rh.ribbon.mgz, filled.mgz, wm.mgz, wm.seg.mgz There is plenty of memory here on the server. But is this maybe an issue with job timing out of server? Otherwise memory and space not an issue. Any help appreciated. Thank you, Anvi On May 25, 2015, at 6:38 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: The error says: mris_fix_topology: could not read input surface /sc/orga/projects/psychimage/MCIC/Schizophrenia/SiteC/Cooked/A00036129/Freesurfer/A00036129/surf/lh.qsphere.nofix No such file or directory Does that file exist? Have you run out of disc space on that volume? doug On 5/22/15 8:11 PM, anvi vora wrote: Hello, So recon-all seems to be running on my Mac fine, with this same data. But it does not run on my institution's Minerva linux server. It did most of volumetric processing steps, but failed on surface processing steps, and then all of the rest. I have checked that environment variables are correct, and they are I believe. Attached is the entire recon-all.log file I will appreciate any help! Thank you very much, Anvi ___ 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 mailto: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 -- 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
Re: [Freesurfer] Custom LookUp Table
This appears to be a problem with the 5.3 version of freeview. I think there is a way to get a newer version. Perhaps Zeke can point it out. doug On 05/26/2015 08:30 AM, Robert Kraft wrote: Doug, Thanks for responding to my question about to a custom lookup table in freeview. My apologies for not responding to the discussion group directly and continuing the thread. I just couldn’t figure out how. All I could find on the Mail Archive was a button to reply to you directly. I am using FreeView. If there are segs not in the color table they will be colorized. I haven’t figured out the pattern yet. This seems odd because there is an Unknown entry in the ColorTable. I just figured if a seg was present in the data but not in the ColorTable it would be colored as Unknown. This is not the case. As a work around I extracted the structures I was interested in and then added them together to create a single seg file with only the structures I wanted. I then used the custom color table and everything was fine. This works well but it requires several additional steps. It certainly would be easier if one could just create a custom lookup table with only the structures of interest. Thanks again for your help, Bob Is that in freeview? I'm not sure what will happen if some segs are not in the colortable. Maybe Roupeng can weigh in. I would like to view just the hippocampus in the aseg.mgz file overlaid with the brain.mgz. I created a custom lookup table by commenting all entries except 0 (Unknown) and 17 (Left-Hippocampus). See below for a snippet of the lookup table. When I load this LookUp table I see numerous structures (7, 8, 10, 12, 13, 14, 41, 47, 51) all labeled with various shades of yellow. Any idea why this is happening? What am I doing wrong? Bob #No. Label Name:R G B A # 0 Unknown 0 0 0 0 ... # 16 Brain-Stem 119 159 176 0 17 Left-Hippocampus220 216 20 0 # 18 Left-Amygdala … ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
Re: [Freesurfer] Longitudinal study: analyze results
Hi Gonzalo, yes, exactly, you only look at the *.long.* folders. Take a look at this page: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics specifically if you have 2 time points for all subjects, you can use the tools for analyzing slopes: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel Cheers, Martin On 05/27/2015 10:29 AM, Gonzalo Rojas Costa wrote: Hi: For example: if I want to compare the volume of left hyppocampus in two time points, could I compare the volume in aseg.stats file of both long folders?... Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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] Longitudinal study: analyze results
Hi: For example: if I want to compare the volume of left hyppocampus in two time points, could I compare the volume in aseg.stats file of both long folders?... Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] differences in subcortical volumes from version 5.1 to 5.3
Hi, We ran our subjects through version 5.1, did a thorough quality check and troubleshoot the data, and then re-ran our subjects through version 5.3 to verify that our findings were consistent between versions. We're running into an issue where we are not able to replicate our subcortical findings from version 5.1 to 5.3. We did not do a similar quality check and troubleshooting process for the 5.3 data, but did not think that would affect the estimation of the subcortical segmentations. Are there any reasons why these subcortical values would be different between both versions? Thanks, Maia ___ 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] FW: correcting for brain size
Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: Thanks for the response, Doug! Yes, here is the error message I get when I try to keep one measure (e.g. ICV or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like keeping both ICV and global volume as nuisance factors) in a simple thickness analysis between two groups, then the analysis is successful. If I only keep one, then QDEC simply closes automatically and I get the attached error. I kept everything qdec outputted for completeness in the attached .txt file. Interestingly, when I run mri_glmfit manually in the terminal, I can pose one measure (e.g global volume) as a covariate without demeaning and the analysis seemingly works (I don't get any errors, anyway). Thank you! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 3:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, sorry for the delay On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote: HI FS experts, I haven’t heard back and am still wrestling with these questions. Any takers? I’d really appreciate any thoughts at all if possible. Thanks, Gabriella *From:*Hirsch, Gabriella *Sent:* Wednesday, May 20, 2015 3:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I’m hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1.So far, I’ve been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to “mean center” the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? It may or may not be a problem depending on what you are doing. I prefer to divide the glm input value by the ICV, but some like to use as a regressor. If you want to do it that way, then you'll have to demean, or you might try to just scale all ICVs to bring them into a range similar to that of the input value. 2.I’ve found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating – is there any way around this issue? Saying that it crashes is not too informative. Can you give more info? Eg, an error message? 3.If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what’s the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I’m executing this correctly. You can scale the input or scale the ICV as I mention above. You can also run it as a DOSS (different offset, same slope) doug I’d really appreciate any help on this. Thank you! Gabriella ___ 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. ___ 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:
Re: [Freesurfer] Apply ROI Label from first time point to longitudinal template
Use mri_label2label. Run it with --help to get more info doug On 05/27/2015 05:08 AM, amirhossein manzouri wrote: Hi All, I have created two ROIs from first time point Qdec group comparison. I need to use this ROI labels to extract the thickness from tp1 and tp2 registered to base (template) subjects(from longitudinal pipeline). Would you please let me how can I convert the label from 1st time point space to longitudinal template space? Best regards, Amirhossein Manzouri -- 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.
[Freesurfer] Longitudinal fMRI analysis
Hi, I have two groups and two time points (pre and post). I want to investigate group*time interactions in an fMRI task taken at both time points. I have run all the subjects through first level FEAT analyses in FSL as well as the longitudinal Freesurfer pipeline. I'm thinking of registering the FEAT first level analyses to the each corresponding longitudinal time point first. Then, if I want to do a group level analysis, can I still use the longitudinal two stage process or is this just designed for structural measures ( http://freesurfer.net/fswiki/LongitudinalTwoStageModel)? Or, would you suggest another approach for group analysis for longitudinal fMRI data taking advantage of Freesurfer? Thanks, Mike Kranz ___ 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] FW: correcting for brain size
Yes, it seems to be a qdec issue since mri_glmfit works by itself even without demeaning the larger values of ICV. Thanks anyway. One unrelated questions since I have you here; does FS produce a total or global cortical surface area file along the lines of TotalGrayVol? I'm looking for the best measure to correct during a group surface area analysis. Thanks again for all your help. Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, May 27, 2015 5:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Oh, sorry, this is not a problem with mri_glmfit as I had thought. It is a problem with qdec itself on your data. I'm not sure what to tell you because I can't debug it without your data (and maybe not even then). You can use mri_glmfit directly. doug On 05/27/2015 04:49 PM, Hirsch, Gabriella wrote: Done. I wasn't sure if I had to put an email address for the recipient so I put yours. Let me know if you figure it out! :) Thanks so much. Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, May 27, 2015 4:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hmm, still can't replicate the error. Can you post this file to our filedrop (see end of msg for url) /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh On 05/27/2015 04:40 PM, Hirsch, Gabriella wrote: Sure. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 4:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size still not sure, can you send these files? /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/ lh-Avg-Intercept-thickness.mat /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/ l h-Diff-EB-control-Intercept-thickness.mat On 05/27/2015 04:30 PM, Hirsch, Gabriella wrote: Sure thing, see attached. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: Thanks for the response, Doug! Yes, here is the error message I get when I try to keep one measure (e.g. ICV or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like keeping both ICV and global volume as nuisance factors) in a simple thickness analysis between two groups, then the analysis is successful. If I only keep one, then QDEC simply closes automatically and I get the attached error. I kept everything qdec outputted for completeness in the attached .txt file. Interestingly, when I run mri_glmfit manually in the terminal, I can pose one measure (e.g global volume) as a covariate without demeaning and the analysis seemingly works (I don't get any errors, anyway). Thank you! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 3:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, sorry for the delay On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote: HI FS experts, I haven't heard back and am still wrestling with these questions. Any takers? I'd really appreciate any thoughts at all if possible. Thanks, Gabriella *From:*Hirsch, Gabriella *Sent:* Wednesday, May 20, 2015 3:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I'm hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1.So far, I've been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to mean center the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? It may or may not be a problem depending on what you are doing. I prefer
Re: [Freesurfer] FW: correcting for brain size
still not sure, can you send these files? /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/lh-Diff-EB-control-Intercept-thickness.mat On 05/27/2015 04:30 PM, Hirsch, Gabriella wrote: Sure thing, see attached. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: Thanks for the response, Doug! Yes, here is the error message I get when I try to keep one measure (e.g. ICV or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like keeping both ICV and global volume as nuisance factors) in a simple thickness analysis between two groups, then the analysis is successful. If I only keep one, then QDEC simply closes automatically and I get the attached error. I kept everything qdec outputted for completeness in the attached .txt file. Interestingly, when I run mri_glmfit manually in the terminal, I can pose one measure (e.g global volume) as a covariate without demeaning and the analysis seemingly works (I don't get any errors, anyway). Thank you! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 3:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, sorry for the delay On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote: HI FS experts, I haven’t heard back and am still wrestling with these questions. Any takers? I’d really appreciate any thoughts at all if possible. Thanks, Gabriella *From:*Hirsch, Gabriella *Sent:* Wednesday, May 20, 2015 3:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I’m hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1.So far, I’ve been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to “mean center” the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? It may or may not be a problem depending on what you are doing. I prefer to divide the glm input value by the ICV, but some like to use as a regressor. If you want to do it that way, then you'll have to demean, or you might try to just scale all ICVs to bring them into a range similar to that of the input value. 2.I’ve found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating – is there any way around this issue? Saying that it crashes is not too informative. Can you give more info? Eg, an error message? 3.If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what’s the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I’m executing this correctly. You can scale the input or scale the ICV as I mention above. You can also run it as a DOSS (different offset, same slope) doug I’d really appreciate any help on this. Thank you! Gabriella ___ 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
Re: [Freesurfer] FW: correcting for brain size
Sure. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 4:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size still not sure, can you send these files? /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/lh-Diff-EB-control-Intercept-thickness.mat On 05/27/2015 04:30 PM, Hirsch, Gabriella wrote: Sure thing, see attached. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: Thanks for the response, Doug! Yes, here is the error message I get when I try to keep one measure (e.g. ICV or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like keeping both ICV and global volume as nuisance factors) in a simple thickness analysis between two groups, then the analysis is successful. If I only keep one, then QDEC simply closes automatically and I get the attached error. I kept everything qdec outputted for completeness in the attached .txt file. Interestingly, when I run mri_glmfit manually in the terminal, I can pose one measure (e.g global volume) as a covariate without demeaning and the analysis seemingly works (I don't get any errors, anyway). Thank you! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 3:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, sorry for the delay On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote: HI FS experts, I haven’t heard back and am still wrestling with these questions. Any takers? I’d really appreciate any thoughts at all if possible. Thanks, Gabriella *From:*Hirsch, Gabriella *Sent:* Wednesday, May 20, 2015 3:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I’m hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1.So far, I’ve been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to “mean center” the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? It may or may not be a problem depending on what you are doing. I prefer to divide the glm input value by the ICV, but some like to use as a regressor. If you want to do it that way, then you'll have to demean, or you might try to just scale all ICVs to bring them into a range similar to that of the input value. 2.I’ve found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating – is there any way around this issue? Saying that it crashes is not too informative. Can you give more info? Eg, an error message? 3.If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what’s the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I’m executing this correctly. You can scale the input or scale the ICV as I mention above. You can also run it as a DOSS (different offset, same slope) doug I’d really appreciate any help on this. Thank you! Gabriella ___ 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:
Re: [Freesurfer] FW: correcting for brain size
Hmm, still can't replicate the error. Can you post this file to our filedrop (see end of msg for url) /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh On 05/27/2015 04:40 PM, Hirsch, Gabriella wrote: Sure. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 4:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size still not sure, can you send these files? /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/lh-Diff-EB-control-Intercept-thickness.mat On 05/27/2015 04:30 PM, Hirsch, Gabriella wrote: Sure thing, see attached. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: Thanks for the response, Doug! Yes, here is the error message I get when I try to keep one measure (e.g. ICV or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like keeping both ICV and global volume as nuisance factors) in a simple thickness analysis between two groups, then the analysis is successful. If I only keep one, then QDEC simply closes automatically and I get the attached error. I kept everything qdec outputted for completeness in the attached .txt file. Interestingly, when I run mri_glmfit manually in the terminal, I can pose one measure (e.g global volume) as a covariate without demeaning and the analysis seemingly works (I don't get any errors, anyway). Thank you! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 3:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, sorry for the delay On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote: HI FS experts, I haven’t heard back and am still wrestling with these questions. Any takers? I’d really appreciate any thoughts at all if possible. Thanks, Gabriella *From:*Hirsch, Gabriella *Sent:* Wednesday, May 20, 2015 3:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I’m hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1.So far, I’ve been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to “mean center” the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? It may or may not be a problem depending on what you are doing. I prefer to divide the glm input value by the ICV, but some like to use as a regressor. If you want to do it that way, then you'll have to demean, or you might try to just scale all ICVs to bring them into a range similar to that of the input value. 2.I’ve found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating – is there any way around this issue? Saying that it crashes is not too informative. Can you give more info? Eg, an error message? 3.If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what’s the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I’m executing this correctly. You can scale the input or scale the ICV as I mention above. You can also run it as a DOSS (different offset, same slope) doug I’d really appreciate any help on this. Thank you! Gabriella ___ 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:
Re: [Freesurfer] FW: correcting for brain size
Done. I wasn't sure if I had to put an email address for the recipient so I put yours. Let me know if you figure it out! :) Thanks so much. Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, May 27, 2015 4:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hmm, still can't replicate the error. Can you post this file to our filedrop (see end of msg for url) /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh On 05/27/2015 04:40 PM, Hirsch, Gabriella wrote: Sure. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 4:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size still not sure, can you send these files? /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/l h-Diff-EB-control-Intercept-thickness.mat On 05/27/2015 04:30 PM, Hirsch, Gabriella wrote: Sure thing, see attached. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: Thanks for the response, Doug! Yes, here is the error message I get when I try to keep one measure (e.g. ICV or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like keeping both ICV and global volume as nuisance factors) in a simple thickness analysis between two groups, then the analysis is successful. If I only keep one, then QDEC simply closes automatically and I get the attached error. I kept everything qdec outputted for completeness in the attached .txt file. Interestingly, when I run mri_glmfit manually in the terminal, I can pose one measure (e.g global volume) as a covariate without demeaning and the analysis seemingly works (I don't get any errors, anyway). Thank you! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 3:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, sorry for the delay On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote: HI FS experts, I haven't heard back and am still wrestling with these questions. Any takers? I'd really appreciate any thoughts at all if possible. Thanks, Gabriella *From:*Hirsch, Gabriella *Sent:* Wednesday, May 20, 2015 3:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I'm hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1.So far, I've been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to mean center the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? It may or may not be a problem depending on what you are doing. I prefer to divide the glm input value by the ICV, but some like to use as a regressor. If you want to do it that way, then you'll have to demean, or you might try to just scale all ICVs to bring them into a range similar to that of the input value. 2.I've found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating - is there any way around this issue? Saying that it crashes is not too informative. Can you give more info? Eg, an error message? 3.If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what's the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I'm executing this correctly. You can scale
Re: [Freesurfer] --sim: Command not found
Right, strictly speaking, permutationis for orthogonal design matrices only, which is not the case when you have a covariate. There was a recent paper by Anderson Winkler Permutation Inference for the General Linear Model in NI in which he goes over various permutation methods for non-orthogonal designs, one of which is to pretend that it is orthogonal (--perm-force). I don't know whether it is appropriate for your design or not. doug On 05/27/2015 04:37 PM, Mihaela Stefan wrote: Thanks! It seems that there was a white space. I ran the permutation command but now I got another error: ERROR: design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with --perm-force Wed May 27 16:27:50 EDT 2015 ERROR: cannot find any csd files I did a group difference like here (first contrast): https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V Best, Mihaela On Wed, May 27, 2015 at 4:18 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Are you sure there is not any white space after the backslash (\)? If so, Can you run it with --debug as the first option? On 05/27/2015 03:39 PM, Mihaela Stefan wrote: Hello FreeSurfers, I am trying to run a clusterwise correction following this link: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis I would like to use the permutation simulation instead of Z Monte Carlo. I ran mri_glmfit-sim --help to get more information. Following an example, I ran this command: mri_glmfit-sim \ --glmdir lh.g2v1.glmdir \ --sim perm 5000 1.3 perm.neg.13 --sim-sign neg Then I got an error which says: --sim: Command not found. I tried again using the exact example in the help info: mri_glmfit-sim --glmdir lh.g2v1.glmdir \ --sim mc-z 1 3 mc-z.neg.3 --sim-sign neg However, I get the same error: --sim: Command not found. Does anyone know why I get this error? Thanks! Mihaela ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto: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 -- 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
Re: [Freesurfer] FW: correcting for brain size
Oh, sorry, this is not a problem with mri_glmfit as I had thought. It is a problem with qdec itself on your data. I'm not sure what to tell you because I can't debug it without your data (and maybe not even then). You can use mri_glmfit directly. doug On 05/27/2015 04:49 PM, Hirsch, Gabriella wrote: Done. I wasn't sure if I had to put an email address for the recipient so I put yours. Let me know if you figure it out! :) Thanks so much. Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, May 27, 2015 4:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hmm, still can't replicate the error. Can you post this file to our filedrop (see end of msg for url) /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh On 05/27/2015 04:40 PM, Hirsch, Gabriella wrote: Sure. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 4:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size still not sure, can you send these files? /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/l h-Diff-EB-control-Intercept-thickness.mat On 05/27/2015 04:30 PM, Hirsch, Gabriella wrote: Sure thing, see attached. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: Thanks for the response, Doug! Yes, here is the error message I get when I try to keep one measure (e.g. ICV or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like keeping both ICV and global volume as nuisance factors) in a simple thickness analysis between two groups, then the analysis is successful. If I only keep one, then QDEC simply closes automatically and I get the attached error. I kept everything qdec outputted for completeness in the attached .txt file. Interestingly, when I run mri_glmfit manually in the terminal, I can pose one measure (e.g global volume) as a covariate without demeaning and the analysis seemingly works (I don't get any errors, anyway). Thank you! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 3:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, sorry for the delay On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote: HI FS experts, I haven't heard back and am still wrestling with these questions. Any takers? I'd really appreciate any thoughts at all if possible. Thanks, Gabriella *From:*Hirsch, Gabriella *Sent:* Wednesday, May 20, 2015 3:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I'm hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1.So far, I've been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to mean center the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? It may or may not be a problem depending on what you are doing. I prefer to divide the glm input value by the ICV, but some like to use as a regressor. If you want to do it that way, then you'll have to demean, or you might try to just scale all ICVs to bring them into a range similar to that of the input value. 2.I've found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating - is there any way around this issue? Saying that it crashes is not too informative. Can you give more info? Eg, an error message? 3.If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what's the best way to go about this? Do I
Re: [Freesurfer] FW: correcting for brain size
Sure thing, see attached. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: Thanks for the response, Doug! Yes, here is the error message I get when I try to keep one measure (e.g. ICV or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like keeping both ICV and global volume as nuisance factors) in a simple thickness analysis between two groups, then the analysis is successful. If I only keep one, then QDEC simply closes automatically and I get the attached error. I kept everything qdec outputted for completeness in the attached .txt file. Interestingly, when I run mri_glmfit manually in the terminal, I can pose one measure (e.g global volume) as a covariate without demeaning and the analysis seemingly works (I don't get any errors, anyway). Thank you! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 3:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, sorry for the delay On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote: HI FS experts, I haven’t heard back and am still wrestling with these questions. Any takers? I’d really appreciate any thoughts at all if possible. Thanks, Gabriella *From:*Hirsch, Gabriella *Sent:* Wednesday, May 20, 2015 3:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I’m hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1.So far, I’ve been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to “mean center” the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? It may or may not be a problem depending on what you are doing. I prefer to divide the glm input value by the ICV, but some like to use as a regressor. If you want to do it that way, then you'll have to demean, or you might try to just scale all ICVs to bring them into a range similar to that of the input value. 2.I’ve found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating – is there any way around this issue? Saying that it crashes is not too informative. Can you give more info? Eg, an error message? 3.If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what’s the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I’m executing this correctly. You can scale the input or scale the ICV as I mention above. You can also run it as a DOSS (different offset, same slope) doug I’d really appreciate any help on this. Thank you! Gabriella ___ 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.
Re: [Freesurfer] --sim: Command not found
Thanks! It seems that there was a white space. I ran the permutation command but now I got another error: ERROR: design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with --perm-force Wed May 27 16:27:50 EDT 2015 ERROR: cannot find any csd files I did a group difference like here (first contrast): https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V Best, Mihaela On Wed, May 27, 2015 at 4:18 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Are you sure there is not any white space after the backslash (\)? If so, Can you run it with --debug as the first option? On 05/27/2015 03:39 PM, Mihaela Stefan wrote: Hello FreeSurfers, I am trying to run a clusterwise correction following this link: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis I would like to use the permutation simulation instead of Z Monte Carlo. I ran mri_glmfit-sim --help to get more information. Following an example, I ran this command: mri_glmfit-sim \ --glmdir lh.g2v1.glmdir \ --sim perm 5000 1.3 perm.neg.13 --sim-sign neg Then I got an error which says: --sim: Command not found. I tried again using the exact example in the help info: mri_glmfit-sim --glmdir lh.g2v1.glmdir \ --sim mc-z 1 3 mc-z.neg.3 --sim-sign neg However, I get the same error: --sim: Command not found. Does anyone know why I get this error? Thanks! Mihaela ___ 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. ___ 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] FS6 DEV Hippocampal Subfield Error
Hi FS Experts,
When I tried to segment the subfields using the Dev version on subjects
that have been previously processed with v5.3, I get the following error:
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Current Stamp: freesurfer-Darwin-mavericks-dev-20150522
INFO: SUBJECTS_DIR is /Users/MacPro/Documents/FS6_hipposubfields_long
Actual FREESURFER_HOME /Applications/freesurfer6
-rw-rw-r-- 1 MacPro staff 1702954 May 6 11:11
/Users/MacPro/Documents/FS6_hipposubfields_long/JT_D372A_3D_A/scripts/recon-all.log
Darwin dhcp-172-17-49-145.wrd.wireless.private.cam.ac.uk 14.0.0 Darwin
Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014;
root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /Applications/freesurfer6
Previous: /Users/fkm24/freesurfer/
#
#@# Hippocampal Subfields processing (T1 only) left Thu May 28 00:34:04 BST
2015
\n /Applications/freesurfer6/bin/segmentSF_T1.sh
/Applications/freesurfer6/MCRv80 /Applications/freesurfer6 JT_D372A_3D_A
/Users/MacPro/Documents/FS6_hipposubfields_long left \n
See log file:
/Users/MacPro/Documents/FS6_hipposubfields_long/JT_D372A_3D_A/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is
/Applications/freesurfer6/lib/gcc/lib:.:/Applications/freesurfer6/MCRv80/runtime/maci64:/Applications/freesurfer6/MCRv80/bin/maci64:/Applications/freesurfer6/MCRv80/sys/os/maci64
dyld: Library not loaded: @rpath/libmwi18n.dylib
Referenced from:
/Applications/freesurfer6/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
Reason: image not found
/Applications/freesurfer6/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
line 40: 54963 Trace/BPT trap: 5
${exe_dir}/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args
#
#@# Hippocampal Subfields processing (T1 only) right Thu May 28 00:34:04
BST 2015
\n /Applications/freesurfer6/bin/segmentSF_T1.sh
/Applications/freesurfer6/MCRv80 /Applications/freesurfer6 JT_D372A_3D_A
/Users/MacPro/Documents/FS6_hipposubfields_long right \n
See log file:
/Users/MacPro/Documents/FS6_hipposubfields_long/JT_D372A_3D_A/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is
/Applications/freesurfer6/lib/gcc/lib:.:/Applications/freesurfer6/MCRv80/runtime/maci64:/Applications/freesurfer6/MCRv80/bin/maci64:/Applications/freesurfer6/MCRv80/sys/os/maci64
dyld: Library not loaded: @rpath/libmwi18n.dylib
Referenced from:
/Applications/freesurfer6/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
Reason: image not found
/Applications/freesurfer6/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
line 40: 55000 Trace/BPT trap: 5
${exe_dir}/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args
#--
Started at Thu May 28 00:34:01 BST 2015
Ended at Thu May 28 00:34:04 BST 2015
#@#%# recon-all-run-time-hours 0.001
recon-all -s JT_D372A_3D_A finished without error at Thu May 28 00:34:05
BST 2015
Any help is greatly appreciated, many thanks!
Best Wishes,
Elijah
--
Elijah Mak,
PhD Candidate *|* Psychiatry
University of Cambridge
Trinity College, Cambridge, CB2 1TQ
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[Freesurfer] FS6 Dev: recon-all error
Hi Freesurfer Experts, I have installed the dev version to test recon-alls on some subjects, but I am running into the following error at the transformation stage. See below for the error message: /Applications/freesurfer6/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig $Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $ Darwin dhcp-172-17-49-145.wrd.wireless.private.cam.ac.uk 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 Thu May 28 00:01:12 BST 2015 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.221 2015/04/16 18:56:00 greve Exp $ reading from orig_nu.mgz... TR=1000.00, 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 -1.0 0.0 0.0 128.0; 0.0 0.0 1.0 -128.0; 0.0 -1.0 0.0 130.0; 0.0 0.0 0.0 1.0; INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Thu May 28 00:01:13 BST 2015 /Applications/freesurfer6/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=3T18yoSchwartzReactN32_as_orig - analyzeto4dfp talsrcimg -O0 -y - $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Thu May 28 00:01:13 2015 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.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-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 - dyld: Library not loaded: /usr/local/lib/libgfortran.3.dylib Referenced from: /Applications/freesurfer6/bin/gauss_4dfp Reason: image not found Trace/BPT trap ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133 ERROR: mpr2mni305 execution aborted Any idea what is happening? There were no such problems in the recon-all with the earlier v5.3 build. Thanks a lot for your help. Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ 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] FW: correcting for brain size
There should be one in aseg.stats. On 05/27/2015 05:45 PM, Hirsch, Gabriella wrote: Yes, it seems to be a qdec issue since mri_glmfit works by itself even without demeaning the larger values of ICV. Thanks anyway. One unrelated questions since I have you here; does FS produce a total or global cortical surface area file along the lines of TotalGrayVol? I'm looking for the best measure to correct during a group surface area analysis. Thanks again for all your help. Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, May 27, 2015 5:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Oh, sorry, this is not a problem with mri_glmfit as I had thought. It is a problem with qdec itself on your data. I'm not sure what to tell you because I can't debug it without your data (and maybe not even then). You can use mri_glmfit directly. doug On 05/27/2015 04:49 PM, Hirsch, Gabriella wrote: Done. I wasn't sure if I had to put an email address for the recipient so I put yours. Let me know if you figure it out! :) Thanks so much. Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, May 27, 2015 4:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hmm, still can't replicate the error. Can you post this file to our filedrop (see end of msg for url) /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh On 05/27/2015 04:40 PM, Hirsch, Gabriella wrote: Sure. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 4:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size still not sure, can you send these files? /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/ lh-Avg-Intercept-thickness.mat /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/ l h-Diff-EB-control-Intercept-thickness.mat On 05/27/2015 04:30 PM, Hirsch, Gabriella wrote: Sure thing, see attached. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: Thanks for the response, Doug! Yes, here is the error message I get when I try to keep one measure (e.g. ICV or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like keeping both ICV and global volume as nuisance factors) in a simple thickness analysis between two groups, then the analysis is successful. If I only keep one, then QDEC simply closes automatically and I get the attached error. I kept everything qdec outputted for completeness in the attached .txt file. Interestingly, when I run mri_glmfit manually in the terminal, I can pose one measure (e.g global volume) as a covariate without demeaning and the analysis seemingly works (I don't get any errors, anyway). Thank you! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 3:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, sorry for the delay On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote: HI FS experts, I haven't heard back and am still wrestling with these questions. Any takers? I'd really appreciate any thoughts at all if possible. Thanks, Gabriella *From:*Hirsch, Gabriella *Sent:* Wednesday, May 20, 2015 3:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I'm hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1.So far, I've been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to mean center the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any
Re: [Freesurfer] Longitudinal fMRI analysis
you can also do a paired analysis (search the wiki) doug On 05/27/2015 05:51 PM, Martin Reuter wrote: Hi Mike, I doubt the 2-stage-model scripts will work for you. They were designed for structural analysis. But you can make use of the within-subject template space to do you fmri analysis (map all fmri results there and do all within-subject comparisons in that space before going across subjects). Mapping stuff to the first time point could potentially bias your results and using the within-subject template (base) will avoid that. Cheers, Martin On 05/27/2015 05:27 PM, Michael Kranz wrote: Hi, I have two groups and two time points (pre and post). I want to investigate group*time interactions in an fMRI task taken at both time points. I have run all the subjects through first level FEAT analyses in FSL as well as the longitudinal Freesurfer pipeline. I'm thinking of registering the FEAT first level analyses to the each corresponding longitudinal time point first. Then, if I want to do a group level analysis, can I still use the longitudinal two stage process or is this just designed for structural measures (http://freesurfer.net/fswiki/LongitudinalTwoStageModel)? Or, would you suggest another approach for group analysis for longitudinal fMRI data taking advantage of Freesurfer? Thanks, Mike Kranz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web :http://reuter.mit.edu ___ 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.
Re: [Freesurfer] Longitudinal fMRI analysis
Hi Mike, I doubt the 2-stage-model scripts will work for you. They were designed for structural analysis. But you can make use of the within-subject template space to do you fmri analysis (map all fmri results there and do all within-subject comparisons in that space before going across subjects). Mapping stuff to the first time point could potentially bias your results and using the within-subject template (base) will avoid that. Cheers, Martin On 05/27/2015 05:27 PM, Michael Kranz wrote: Hi, I have two groups and two time points (pre and post). I want to investigate group*time interactions in an fMRI task taken at both time points. I have run all the subjects through first level FEAT analyses in FSL as well as the longitudinal Freesurfer pipeline. I'm thinking of registering the FEAT first level analyses to the each corresponding longitudinal time point first. Then, if I want to do a group level analysis, can I still use the longitudinal two stage process or is this just designed for structural measures (http://freesurfer.net/fswiki/LongitudinalTwoStageModel)? Or, would you suggest another approach for group analysis for longitudinal fMRI data taking advantage of Freesurfer? Thanks, Mike Kranz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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.
