Freesurfer October 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
244 discussions

possible pial surface editing
by Gennan Chen 05 Dec '13

05 Dec '13

Hi! All, We ran into a few cases which the wm matter surface is pretty decent but pial surface did not go far enough to include all gray matter. Is there a way to fix this? Gen ________________________________ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator

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Re: [Freesurfer] [martinos-tech] FSFAST between-conditions contrasts
by Douglas N Greve 04 Dec '13

04 Dec '13

Hi Sue, that looks correct. I think it is an open question as to whether you should use the corrected maps or use the uncorrected and then correct the final map. Maybe someone else can chime in. doug On 10/23/2013 09:49 AM, Susan Ruiz wrote: > Hi Doug, > > This is /very/ helpful. > > Procedurally, would this be the correct approach? > > For positive % signal change from baseline clusters, use these files > resulting from mri_glmfit-sim: > condAvFix.th3.pos.sig.cluster.nii > condBvFix.th3.pos.sig.cluster.nii > condAvscondB.th3.pos.sig.cluster.nii > > then run: > % mri_concat --i condAvFix.th3.pos.sig.cluster.nii --i > condBvFix.th3.pos.sig.cluster.nii --i > condAvscondB.th3.pos.sig.cluster.nii --conjunct --o positive.AvsB.nii > > For negative % signal change from baseline clusters, use these files > resulting from mri_glmfit-sim: > condAvFix.th3.neg.sig.cluster.nii > condBvFix.th3.neg.sig.cluster.nii > condAvscondB.th3.pos.sig.cluster.niigrf.th3.pos.sig.cluster.nii > > then run: > % mri_concat --i condAvFix.th3.neg.sig.cluster.nii --i > condBvFix.th3.neg.sig.cluster.nii --i > condAvscondB.th3.pos.sig.cluster.nii --conjunct --o negative.AvsB.nii > > Note that for positive activation differences I would use sign=pos for > each condition vs fixation during mri_glmfit-sim, and for > "deactivation" clusters I use sign=neg for each condition vs fixation > during mri_glmfit-sim. BUT for both cases I use sign=pos for condition > A vs. condition B. > > Thanks so much! > > Best, > ~Sue > > > > On Tue, Oct 22, 2013 at 10:50 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Sue, I agree that they are not the same thing. There is not a > single > flag that will do what you want. What you are describing is a post-hoc > test. So you look for places where A != B, then within those > voxels you > do posthoc tests. You can implement this with a conjunction analysis > where you set up threeway conjunction A>B and A>0 and B>0. You can do > this with the --conjunt option to mri_concat > doug > > > On 10/21/2013 02:13 PM, Susan Ruiz wrote: > > Hi all, > > > > When running a functional analysis and comparing two experimental > > conditions, we observed that there are some voxels/vertices > where both > > condition A and condition B have a positive % signal change from > > baseline, and condition A has greater activity than condition B. > > > > In other regions, both condition A and condition B have negative % > > signal change from baseline, but condition B has a greater absolute > > value % signal change (thus relative to baseline condition B has > more > > "deactivation"--a term I am using since you all know what I mean > even > > if the term itself is imperfect). > > > > Since, in both cases, the % signal change is technically > condition A > > > condition B, the between-conditions maps do not distinguish > these two > > scenarios. FS-FAST sees these as being the same. Is there a way to > > tell FS-FAST to cluster these scenarios separately? Is there a > > compelling reason why I should not consider these different > > situations? It seems to me that the interpretation of what's taking > > place in these two scenarios is not identical. Agree or > disagree? Can > > FS-FAST distinguish these with a flag I don't know about? > > > > Thank you, > > ~Sue > > > > -- > > * * ** *** ***** ******** ************* > > Susan Mosher Ruiz, Ph.D. > > Research Scientist > > Boston University School of Medicine > > Laboratory of Neuropsychology > > VA Boston Healthcare System > > smosher(a)bu.edu <mailto:smosher@bu.edu> <mailto:smosher@bu.edu > <mailto:smosher@bu.edu>> > > * * ** *** ***** ******** ************* > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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/ > > > > 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. > > > > ------------------------------------ > > Yahoo! Groups Links > > <*> To visit your group on the web, go to: > http://groups.yahoo.com/group/martinos-tech/ > > <*> Your email settings: > Individual Email | Traditional > > <*> To change settings online go to: > http://groups.yahoo.com/group/martinos-tech/join > (Yahoo! ID required) > > <*> To change settings via email: > martinos-tech-digest(a)yahoogroups.com > <mailto:martinos-tech-digest@yahoogroups.com> > martinos-tech-fullfeatured(a)yahoogroups.com > <mailto:martinos-tech-fullfeatured@yahoogroups.com> > > <*> To unsubscribe from this group, send an email to: > martinos-tech-unsubscribe(a)yahoogroups.com > <mailto:martinos-tech-unsubscribe@yahoogroups.com> > > <*> Your use of Yahoo! Groups is subject to: > http://info.yahoo.com/legal/us/yahoo/utos/terms/ > > > > > -- > * * ** *** ***** ******** ************* > Susan Mosher Ruiz, Ph.D. > Research Scientist > Boston University School of Medicine > Laboratory of Neuropsychology > VA Boston Healthcare System > smosher(a)bu.edu <mailto:smosher@bu.edu> > * * ** *** ***** ******** ************* > __._,_.___ > Reply via web post > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJwa21mMTlwBF9TA…> > Reply to sender > <mailto:smosher@bu.edu?subject=Re%3A%20%5Bmartinos-tech%5D%20FSFAST%20between-conditions%20contrasts> > Reply to group > <mailto:martinos-tech@yahoogroups.com?subject=Re%3A%20%5Bmartinos-tech%5D%20FSFAST%20between-conditions%20contrasts> > Start a New Topic > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJlZjd2ZDVnBF9TA…> > Messages in this topic > <http://groups.yahoo.com/group/martinos-tech/message/5844;_ylc=X3oDMTM0a2Nkb…> > (3) > > Recent Activity: > > Visit Your Group > <http://groups.yahoo.com/group/martinos-tech;_ylc=X3oDMTJlcXY1cjhnBF9TAzk3Mz…> > > Yahoo! Groups > <http://groups.yahoo.com/;_ylc=X3oDMTJkdW8xcWpkBF9TAzk3NDc2NTkwBGdycElkAzQ5O…> > > Switch to: Text-Only > <mailto:martinos-tech-traditional@yahoogroups.com?subject=Change%20Delivery%20Format:%20Traditional>, > Daily Digest > <mailto:martinos-tech-digest@yahoogroups.com?subject=Email%20Delivery:%20Digest> > • Unsubscribe > <mailto:martinos-tech-unsubscribe@yahoogroups.com?subject=Unsubscribe> > • Terms of Use <http://info.yahoo.com/legal/us/yahoo/utos/terms/> • > Send us Feedback > <mailto:ygroupsnotifications@yahoogroups.com?subject=Feedback%20on%20the%20redesigned%20individual%20mail%20v1> > . > > __,_._,___ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Error when using --mask flag in mri_glmfit
by Suzanne Oosterwijk 14 Nov '13

14 Nov '13

Hello all, I want to run a Monte Carlo simulation within a volume ROI and I am running into a problem when I use the --mask flag while running glmfit. My question is very similar to the question asked in "[Freesurfer] Volume-based Monte Carlo Restricted to a within mask area" but I could not find the response to this question. Here is my code. First, I created a volume mask with mri_binarize: mri_binarize --match 18 --i home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri/aseg.mgz --o /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz I checked the mask and it looked good. Then I use the mask in glmfit. mri_glmfit --y ces.nii.gz --osgm --glmdir glm.amygdala_lh --mask /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz When I do this, I get the following error: ERROR: dimension mismatch 1 between y and mask I guess this means that the ces.nii.gz file and mask file don't match, but I have no idea how to solve this. Any thoughts? Thanks! Suzanne -- Suzanne Oosterwijk, Ph.D. Postdoctoral Researcher Department of Social Psychology University of Amsterdam s.oosterwijk@u <s.oosterwijk(a)neu.edu>va.nl https://sites.google.com/site/suzanneoosterwijk/

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longitudinal measures
by Qi Wu 06 Nov '13

06 Nov '13

Hi Freesurfer users, For the longitudinal stream in FS5.1, there are only 4 options of measures (do-avg, do-rate, do-pc1 and do-spc). However, if I need other measures, such as the difference between two time points (thick2-thick1), how should I do to get the values and still be able to do the voxel-wise analysis for regional difference in cortical thickness (with glmfit)? Many thanks Keith Postdoc research fellow Toronto Western Hospital 1. The temporal average is simply the average thickness: *avg = 0.5 * (thick1 + thick2)* 2. The rate of change is the difference per time unit, so *rate = ( thick2 - thick1 ) / (time2 - time1)*. 3. The percent change (pc1) is the rate with respect to the thickness at the first time point: *pc1 = rate / thick1*. 4. The symmetrized percent change (spc) is the rate with respect to the average thickness: *spc = rate / avg*.

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Re: [Freesurfer] How do you create labels from binary masks?
by Douglas N Greve 06 Nov '13

06 Nov '13

areyou loading the label (output of mri_cor2label) or did you create an annotation? Try loading the label. Then try loading LeftHippoBody_surf.mgh. If that does not look ok, check the registration between binLeftHippoBody.mgz and subj1 with --regheader doug On 10/24/2013 06:40 PM, Marcos Martins da Silva wrote: > Hi, Doug > Thanks again for your help. > Using the command tksurfer suj1 lh surfHippo, I get the surface loaded > in tksurfer in the same way that I get in freeview. The only > difference is that the terminal window output is more verbose and that > is valuable when investigating this kind of situation. I am attaching > a screenshot. I got this just after I used tksurfer to import an > annotation (lh.surfHippo + hippo.annot.png). > The screenshot show just a few vertices with color. Indeed this is > similar to what we see in freeview, except that in this last tool all > vertices not in label appears in black and tksurfer preserves the gray > color. > At terminal output we can see tksurfer expects the surface refers to > lh.white. That is not the case, I guess. I think it helps explain the > terminal window output we see in freeview and also in tksurfer when I > try to load the annot file. It seems we have lots of vertices in annot > file that both tools cannot find in surface file and at the same time > we have lots of vertices in my surface file not described in the annot > files. At least now I can understand the situation. It puzzles me > because the surface, binary masks, labels and annotations were created > from the same source: the posterior*.mgz files created by recon-all > --hippo-subfields. But, well, I probably misunderstood something in > documentation and lost my way in some point. I hope you can help me > with the correct steps to be followed. I still dream of showing the > hippocampus in a similar way we do with cortex when we load lh.pial > and lh.aparc.annot. > Thank you for your help and attention. > Cheers, > Marcos. > Em Qui, 2013-10-24 às 12:40 -0400, Douglas N Greve escreveu: >> Can you load it properly in tksurfer? >> >> >> On 10/23/2013 12:44 AM, Marcos Martins da Silva wrote: >> > >> > Hi, Doug >> > Sorry for this late feedback. >> > Just so you can understand what is binLeftHippoBody.mgz I will explain >> > its origin. >> > 1) recon-all --hippo-subfields >> > 2) mri_concat the posterior*.mgz to get the whole hippocampus >> > 3) a custom octave routine to segment the whole hippocampus into head, >> > body and tail. This routine preserves the probability values of the >> > original posterior*.mgz >> > 4) mri_binarize the whole hippocampus and its segments. So >> > binLeftHippoBody.mgz is the binary mask of left hippocampal body. >> > 5) mri-tesselate and mris_smooth the whole hippocampus binary mask to >> > create a surface (lh.surfHippo) >> > >> > Now that is the reason I would like to get the surface labels for >> > head, body and tail. I would like to build a annot in order to display >> > the colored segments over the whole hippocampus surface. >> > Your last tip was great and now I have vertex numbers at the labels >> > files and mris_label2annot works. It follows the commands I used to >> > process the hippocampal body: >> > mri_vol2surf --src binLeftHippoBody.mgz --out LeftHippoBody_surf.mgh >> > --out_type mgh --hemi lh --regheader suj1 --surf surfHippo >> > mri_cor2label --i LeftHippoBody_surf.mgh --surf suj1 lh surfHippo --id >> > 1 --l lh.HippoBody.label >> > >> > I put the --surf parameter pointing to lh.surfHippo because, if not, >> > it would use lh.white (default). As I said it works but the results >> > are not visually correct (see attached file). The surface loads on >> > freeview with no problem but if I try to load the label representing >> > the body or the annot with the 3 segments they do not appear. It seems >> > only a small part of the vertices appears in blue. I also get the >> > following output at the terminal window I used to start freeview: >> > >> > MRISreadAnnotationIntoArray: vertex index out of range: 122882 >> > i=00000000, in_array_size=11627 >> > annot file: ../label/lh.Hippo.annot >> > MRISreadAnnotationIntoArray: vertex index out of range: 122883 >> > i=00000000, in_array_size=11627 >> > annot file: ../label/lh.Hippo.annot >> > MRISreadAnnotationIntoArray: vertex index out of range: 122884 >> > i=00000000, in_array_size=11627 >> > annot file: ../label/lh.Hippo.annot >> > MRISreadAnnotationIntoArray: vertex index out of range: 122885 >> > i=00000000, in_array_size=11627 >> > annot file: ../label/lh.Hippo.annot >> > reading colortable from annotation file... >> > colortable with 4 entries read (originally ../label/Hippo.ctab) >> > colortable with 4 entries read (originally ../label/Hippo.ctab) >> > =00000000, in_array_size=11627 >> > >> > Since the posterior*.mgz files are 0.5 x 0.5 x 0.5 mm I also tried to >> > use mri_convert --vs 1 1 1, but it did not worked too. >> > I guess, or at least, I hope I am closer the image I want but I guess >> > some more steps are necessary. >> > Thank you for any help. >> > Marcos >> > >> > >> > >> > Em Qui, 2013-10-17 às 22:19 -0400, Douglas Greve escreveu: >> >> >> >> Is *binLeftHippoBody.mgz a volume label or a surface label? If a >> >> volume label, map it onto the surface with mri_vol2surf, the run >> >> mri_cor2label *specifying --surf >> >> >> >> doug >> >> >> >> >> >> >> >> >> >> On 10/17/13 5:00 PM, Marcos Martins da Silva wrote: >> >> >> >>> Hi, Doug >> >>> Thank you for your answer. >> >>> >> >>> I am trying cor2label as you suggested. First of all I am afraid to >> >>> say that website documentation and help from the own command are a >> >>> bit different so I got a little confused. But the following command >> >>> worked: *mri_cor2label --i binLeftHippoBody.mgz --id 1 --l 2.leftBody* >> >>> >> >>> Using freeview I could load the hippocampus volume and 2.leftBody as >> >>> a ROI. I attached a screenshot that also included 1.leftHead and >> >>> 3.leftTail, generated in the same way. >> >>> When I tried to concatenate the 3 labels into an annot file I got an >> >>> error: >> >>> >> >>> *mris_label2annot --s bert --h lh --ctab HippoColorLUT.txt --l >> >>> 1.leftHead.label --l 2.leftBody.label --l 3.leftTail.label --a >> >>> lefthippo* >> >>> *Loading /home/marcos/freesurfer/subjects/bert/surf/lh.orig* >> >>> *1 16711680 leftHead* >> >>> *ERROR: 1.leftHead.label, n=0, vertex -1 out of range* >> >>> >> >>> When I checked label file generated by mri_cor2label the first >> >>> collumn (vertex number) contains only *-1* as value. >> >>> It seems that when you use mri_cor2label it does not preserve or >> >>> even recover the vertex number. It also seems I need the correct >> >>> vertex number in label file to use mris_label2annot >> >>> Just to rule out a problem with the hippocampal subfield files I >> >>> tried the example command (extracted from command help): >> >>> mri_cor2label --i aseg.mgz --id 12 --l left-putamen.label >> >>> This label also shows only -1 as vertex number. >> >>> >> >>> Could you please explain me what do I need to do to get the vertex >> >>> numbers in the label file as output of mri_cor2label? >> >>> >> >>> Cheers, >> >>> Marcos >> >>> >> >>> >> >>> >> >>> Em Qua, 2013-10-16 às 20:34 -0400, Douglas Greve escreveu: >> >>>> I think you need to use mri_cor2label (not very well named:) >> >>>> doug >> >>>> >> >>>> >> >>>> On 10/16/13 4:24 PM, Marcos Martins da Silva wrote: >> >>>> >> >>>>> Hi, Freesurfers. >> >>>>> I need to create some labels from binary masks. Sometime ago I >> >>>>> read a post >> >>>>> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-October/033783.… >> >>>>> ) and, unless I am wrong, it seemed to me that mri_label2vol could >> >>>>> be the tool to get it. If so, could you please explain how? I >> >>>>> read documentation on wiki and help from the command itself and >> >>>>> could not see how to accomplish that. I could only find how to >> >>>>> create a volume from a label. What I need to do is to get a mask >> >>>>> like the binLeftHippoHead.mgz (attached) and create a label. >> >>>>> Assuming it is possible, I could also make labels for Hippocampal >> >>>>> body and head, merge the 3 labels into an annot file. This way i >> >>>>> can use Freeview to load the whole hippocampal surface and >> >>>>> discriminate the 3 segments by colors with the annot file. >> >>>>> Thanks in advance for any help. >> >>>>> Cheers, >> >>>>> Marcos. >> >>>>> >> >>>>> _______________________________________________ >> >>>>> Freesurfer mailing list >> >>>>>Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >>>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>>> >> >>>> _______________________________________________ >> >>>> Freesurfer mailing list >> >>>>Freesurfer(a)nmr.mgh.harvard.edu <mailto: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. >> >>> >> >> >> > >> > >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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LGI path problem
by Linn Mittlestein 05 Nov '13

05 Nov '13

Hi, I am trying to compute lgi measures, and I think my problem lies in the fact that the matlab path is not set correctly; it is calling an older version of matlab however I need it to point to matlab2013b. I have tried numerous things like changing the startup.m file, the .bashrc file and exporting the matlab path, however It keeps calling another version of Matlab. Can someone please tell me how exactly the path is set and where? Best Wishes and thank you, Linn

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glmfit for paired-diff on 2 groups
by Vivian R. Steiger 04 Nov '13

04 Nov '13

Dear FS-Experts, I would like to compare 2 Groups (Responder (N=19) vs. Non-Responder (N=11)) with longitudinal data. Participants from both groups had only 2 scan sessions in each case 10 weeks apart. So far is used the glmfit-variant with --paired-diff option in the first place. (based on http://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis) The paired-fsgd contained then 2 classes (Responder, Non-Responder) which is used in glm-fit for comparison with the contrast (1 -1) for group diffs. This approach confirmed our hypothesized effects but I'm not sure whether I used the right strategy. Could you might help me with this issue? Thank in advance Best, Vivian

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mri_segstats url in 5.3.0 release notes does not exist
by Jonathan Harlap 04 Nov '13

04 Nov '13

The version of mri_segstats that fixes the issue where mri_segstats fails unless -autorecon3 is run returns a file not found at the url ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats. Is there a source that the release notes should refer to and which will not disappear, or can it be restored? Cheers, Jonathan

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Fwd: Qdec Questions
by Ashley Shurick 04 Nov '13

04 Nov '13

Great - and this would be true for all models? For example, in the attached graph, I'm looking at a region representing increased cortical thickness for one group compared to the other (orange blob, Q: "Does the average thickness differ between HC and SAD?" nuisance factor: mean thickness). From this plot it appears that SAD > HC, but based on your answer to the previous question I would think this region should represent HC > SAD. Can you please explain this? Thank you! On Wed, Oct 30, 2013 at 7:33 AM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > > In your case you have HC listed first, so red/yellow means HC>SAD, blue > means SAD>HC > doug > > > > > > > On 10/29/2013 11:03 PM, Ashley Shurick wrote: > >> Hi Doug, >> >> Apologies, but I have a rather easy follow-up question that I can't >> figure out: >> >> How do you interpret the effect in each significant region? A previous >> post suggests using ctrl + left mouse click on a blob and examining the >> plot of the data. However, for the model I am looking at ("Does the >> thickness-ERQ correlation differ between HC and SAD?") I still can't >> determine if cortical thinning represents HC<SAD or SAD<HC. I'm attaching a >> representative plot here. >> >> Thank you, >> >> Ashley >> >> >> On Tue, Oct 29, 2013 at 10:25 AM, Ashley Shurick < >> ashley.shurick(a)gmail.com <mailto:ashley.shurick@gmail.**com<ashley.shurick(a)gmail.com>>> >> wrote: >> >> Thank you! >> >> >> On Tue, Oct 29, 2013 at 10:19 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>> >> wrote: >> >> >> On 10/29/2013 01:10 PM, Ashley Shurick wrote: >> > Hi all, >> > >> > I'm running analyses in Qdec and want to verify a few things: >> > >> > 1. When comparing two groups (HC vs patients) I am including >> mean >> > cortical thickness as a covariate, using the following equation: >> > >> > >> > bh.thickness = (lh.thickness*lh.surfarea + >> rh.thickness*rh.surfarea) / >> > (lh.surfarea + rh.surfarea) >> > >> > >> > Is this the best way to calculate global mean thickness? >> Yes >> > >> > >> > 2. I want to regress out any effects of age, therefore I need to >> > demean the ages for my groups as a whole, and not perform this >> > calculation on each group separately, correct? >> Yes, in which case the test of the difference between groups >> will be >> done at an age equal to the mean of the ages. >> > >> > 3. I'm including questionnaires as a covariate of interest - >> do I need >> > to demean these values as well? >> When you do a test on a continuous covariate, that test will be >> unaffected by demeaning of the covariate. Demeaning will >> affect the >> difference between groups if you use a separate covariate for each >> group. If you have a single covariate across groups, demeaning >> will have >> no effect. >> >> doug >> > >> > >> > Thank you in advance for your help! >> > >> > >> > Ashley >> > >> > >> > -- >> > Ashley A. Shurick >> > Ph.D. Candidate >> > Department of Psychology >> > Stanford University >> > >> > >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> >> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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> >> <http://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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >> >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 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<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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >

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mri_segment WM/GM limits
by Jonathan Holt 04 Nov '13

04 Nov '13

HI experts, I’m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number? Jon

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Freesurfer October 2013