[Freesurfer] Question about design matrix for surface group analysis
External Email - Use Caution Dear freesurfer users, I have a question about the design matrix.We want to analyse the relationship between the cortical thickness and the neuropsychological test. We have two groups:TLE and extralTLE,one discrete variable:gender,and two continuous variable: neuropsychological test and age. we make the FSGD files like this:Title OSGM Class MaleTLE Class MaleextraTLE Class FemaleTLE Class FemaleexatrTLE Variables Age Neuropsychology Input subject1 MaleTLE 30 5 Input subject2 MaleextraTLE 40 6 Input subject3 FemaleTLE 50 8 Input subject4 FemaleLextraTLE 60 7 Is it right? And we want to analyze the relationship between the cortical thickness and the neuropsychology regressing out the effects of gender and age, how to make the design matrix? Look forward to your reply. Sincerely, Kan Deng___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS
Sure, if you have enough ram and cores > On Nov 7, 2019, at 10:23 PM, Emanuel Alvaredo wrote: > > External Email - Use Caution > > Hi Bruce, same result. > > Question, Is it possible run two recon-all at the same time? > > Emanuel > > >> On Thu, Nov 7, 2019 at 4:41 PM Bruce Fischl >> wrote: >> hmmm, does it always happen for this subject? What if you don't use >> -parallel? >> On Thu, 7 Nov 2019, Emanuel Alvaredo wrote: >> >> > >> > External Email - Use Caution >> > >> > Hi Bruce! Thanks for answer!! >> > * The command line is >> > >> > recon-all -s SUBJECT_NAME -i >> > /patients/SUBJECT_NAME/2_COGNITIVO/4_Accelerated_Ax_IR-FSPGR/i1602413.MRDC.127 >> > -all -parallel >> > >> > >> > >> > * In this mail is attached the log. There is >> > >> > Segmentation fault (core dumped) >> > >> > * This happens running when I call a process from a Java application, but >> > too if I run the >> > command manually. >> > >> > >> > >> > I think this is the problem, but I dont know why. >> > >> > Thanks in advance >> > >> > >> > Emanuel >> > >> > >> > On Wed, Oct 30, 2019 at 10:51 AM Bruce Fischl >> > wrote: >> > Hi Emanuel >> > >> > can you give us more details. What was your command line? What was >> > the >> > full job output? What is in the recon-all.log? Does this happen if >> > you >> > run directly instead of through some type of batch server? >> > >> > cheers >> > Bruce >> > On Wed, 30 Oct >> > 2019, Emanuel Alvaredo wrote: >> > >> > > >> > > External Email - Use Caution >> > > >> > > Hello Developers! >> > > I am getting the same error in several patients (not all). The >> > common error >> > > between all of them is this line >> > > >> > > Waiting for PID 2778 of (2778 2781) to complete... >> > > /usr/local/freesurfer/bin/reconbatchjobs: line 81: 2778 >> > Segmentation fault >> > > (core dumped) exec $JOB >> $LOG 2>&1 >> > > Waiting for PID 2781 of (2778 2781) to complete... >> > > >> > > Any idea? >> > > >> > > Thanks in advance! >> > > >> > > >> > > >> > > Emanuel >> > > >> > > >> > > On Tue, Oct 1, 2019 at 5:07 PM Emanuel Alvaredo >> > wrote: >> > > >> > > Hello FreeSurfer Developers, >> > > >> > > I am running de following command >> > > /usr/local/freesurfer/subjects/SOME_SUBJECT >> > > /usr/local/freesurfer/bin/recon-all >> > > -s SOME_SUBJECT -i >> > /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_ >> > > FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 - >> > > all -parallel >> > > I've searched the list and no similar errors have been reported. >> > Does anyone >> > > have any thoughts on how to trouble-shoot this one? Also, Ive >> > attached the >> > > recon-all.log in case it's of any use. >> > > I have checked the log but I dont find de cause. >> > > >> > > 1) FreeSurfer >> > version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb >> > > 96c >> > > 2) Platform:Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz >> > > 3) uname -a: Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu >> > SMP Thu S >> > > ep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux >> > > 4) recon-all.log: see attached >> > > Thanks in advance >> > > Emanuel >> > > >> > > >> > >___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> >___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS
External Email - Use Caution Hi Bruce, same result. Question, Is it possible run two recon-all at the same time? Emanuel On Thu, Nov 7, 2019 at 4:41 PM Bruce Fischl wrote: > hmmm, does it always happen for this subject? What if you don't use > -parallel? > On Thu, 7 Nov 2019, Emanuel Alvaredo wrote: > > > > > External Email - Use Caution > > > > Hi Bruce! Thanks for answer!! > > * The command line is > > > > recon-all -s SUBJECT_NAME -i > > > /patients/SUBJECT_NAME/2_COGNITIVO/4_Accelerated_Ax_IR-FSPGR/i1602413.MRDC.127 > -all -parallel > > > > > > > > * In this mail is attached the log. There is > > > > Segmentation fault (core dumped) > > > > * This happens running when I call a process from a Java application, > but too if I run the > > command manually. > > > > > > > > I think this is the problem, but I dont know why. > > > > Thanks in advance > > > > > > Emanuel > > > > > > On Wed, Oct 30, 2019 at 10:51 AM Bruce Fischl < > fis...@nmr.mgh.harvard.edu> wrote: > > Hi Emanuel > > > > can you give us more details. What was your command line? What was > the > > full job output? What is in the recon-all.log? Does this happen if > you > > run directly instead of through some type of batch server? > > > > cheers > > Bruce > > On Wed, 30 Oct > > 2019, Emanuel Alvaredo wrote: > > > > > > > > External Email - Use Caution > > > > > > Hello Developers! > > > I am getting the same error in several patients (not all). The > common error > > > between all of them is this line > > > > > > Waiting for PID 2778 of (2778 2781) to complete... > > > /usr/local/freesurfer/bin/reconbatchjobs: line 81: 2778 > Segmentation fault > > > (core dumped) exec $JOB >> $LOG 2>&1 > > > Waiting for PID 2781 of (2778 2781) to complete... > > > > > > Any idea? > > > > > > Thanks in advance! > > > > > > > > > > > > Emanuel > > > > > > > > > On Tue, Oct 1, 2019 at 5:07 PM Emanuel Alvaredo < > ealvar...@gmail.com> wrote: > > > > > > Hello FreeSurfer Developers, > > > > > > I am running de following command > > > /usr/local/freesurfer/subjects/SOME_SUBJECT > > > /usr/local/freesurfer/bin/recon-all > > > -s SOME_SUBJECT -i > /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_ > > > FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 - > > > all -parallel > > > I've searched the list and no similar errors have been reported. > Does anyone > > > have any thoughts on how to trouble-shoot this one? Also, Ive > attached the > > > recon-all.log in case it's of any use. > > > I have checked the log but I dont find de cause. > > > > > > 1) FreeSurfer > version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb > > > 96c > > > 2) Platform:Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz > > > 3) uname -a: Linux fisicos-ub2 5.0.0-29-generic > #31~18.04.1-Ubuntu SMP Thu S > > > ep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux > > > 4) recon-all.log: see attached > > > Thanks in advance > > > Emanuel > > > > > > > > >___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] T2 white matter surface refinement
External Email - Use Caution Hi, Looking through the documentation, there are extra options to include a T2 image to refine the pial surface boundary, but I was wondering if FreeSurfer can use a T2 in conjunction with a T1 to help refine the white matter/gray matter boundary? As in, gray matter with higher myelin content than average could cause the white matter boundary to be placed further out than normal when just using a T1; can FreeSurfer currently use a T2 image to help prevent that at all? Thank you -Matt Matthew K. Defenderfer B.S. | Graduate Research Assistant Graduate Biomedical Sciences | Neuroscience UAB | The University of Alabama at Birmingham Laboratory of Kristina Visscher, PhD Department of Neurobiology ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS
hmmm, does it always happen for this subject? What if you don't use -parallel? On Thu, 7 Nov 2019, Emanuel Alvaredo wrote: External Email - Use Caution Hi Bruce! Thanks for answer!! * The command line is recon-all -s SUBJECT_NAME -i /patients/SUBJECT_NAME/2_COGNITIVO/4_Accelerated_Ax_IR-FSPGR/i1602413.MRDC.127 -all -parallel * In this mail is attached the log. There is Segmentation fault (core dumped) * This happens running when I call a process from a Java application, but too if I run the command manually. I think this is the problem, but I dont know why. Thanks in advance Emanuel On Wed, Oct 30, 2019 at 10:51 AM Bruce Fischl wrote: Hi Emanuel can you give us more details. What was your command line? What was the full job output? What is in the recon-all.log? Does this happen if you run directly instead of through some type of batch server? cheers Bruce On Wed, 30 Oct 2019, Emanuel Alvaredo wrote: > > External Email - Use Caution > > Hello Developers! > I am getting the same error in several patients (not all). The common error > between all of them is this line > > Waiting for PID 2778 of (2778 2781) to complete... > /usr/local/freesurfer/bin/reconbatchjobs: line 81: 2778 Segmentation fault > (core dumped) exec $JOB >> $LOG 2>&1 > Waiting for PID 2781 of (2778 2781) to complete... > > Any idea? > > Thanks in advance! > > > > Emanuel > > > On Tue, Oct 1, 2019 at 5:07 PM Emanuel Alvaredo wrote: > > Hello FreeSurfer Developers, > > I am running de following command > /usr/local/freesurfer/subjects/SOME_SUBJECT > /usr/local/freesurfer/bin/recon-all > -s SOME_SUBJECT -i /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_ > FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 - > all -parallel > I've searched the list and no similar errors have been reported. Does anyone > have any thoughts on how to trouble-shoot this one? Also, Ive attached the > recon-all.log in case it's of any use. > I have checked the log but I dont find de cause. > > 1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb > 96c > 2) Platform:Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz > 3) uname -a: Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu S > ep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux > 4) recon-all.log: see attached > Thanks in advance > Emanuel > > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Help with "orig.mgz"
External Email - Use Caution Thanks you Bruce El jue., 7 de nov. de 2019 12:18, Bruce Fischl escribió: > Hi Fernando > > it is a volume after resampling to 1mm isotropic, 8 bits/voxel and 256^3 > > cheers > Bruce > On > Thu, 7 Nov 2019, Fernando Castellano wrote: > > > > > External Email - Use Caution > > > > good afternoon, > > I am using freesurfer for my thesis in image technician. > > I would like to know specifically what the orig.mgz file is? > > I have read that it is step 1 of re-conall. But I don't fully understand > > > > thank you, best regards > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Help with "orig.mgz"
Hi Fernando it is a volume after resampling to 1mm isotropic, 8 bits/voxel and 256^3 cheers Bruce On Thu, 7 Nov 2019, Fernando Castellano wrote: External Email - Use Caution good afternoon, I am using freesurfer for my thesis in image technician. I would like to know specifically what the orig.mgz file is? I have read that it is step 1 of re-conall. But I don't fully understand thank you, best regards ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Help with "orig.mgz"
External Email - Use Caution good afternoon, I am using freesurfer for my thesis in image technician. I would like to know specifically what the orig.mgz file is? I have read that it is step 1 of re-conall. But I don't fully understand thank you, best regards ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] LME model contrast matrix (Diers, Kersten /DZNE)
External Email - Use Caution Hello Guodong, On Mi, 2019-11-06 at 11:28 +0800, Liu Guodong wrote: > External Email - Use Caution > > Hi Kersten, > > Thank you so much for the reply and that helps a lot. > > There are still some questions that I hope you can help me. > > 1.For the first model in you last email, you said 'To get the > mean for group B, one would need to add the beta weights of the two > regressors.’. I wonder if the beta weights should be 1 for > regressors1 and 1 for regressor2, and the mean for group B is > regressor2 plus regressor1 with the condition the value of group B is > bigger than group A. I am not sure if I understand correctly, but I suppose what you have in mind is the contrast weights rather than the beta weights. With beta weights I am referring to the parameters estimated by the model (beta values), so you can't specify those. With contrast weights I am referring to the elements of the contrast vector or matrix (often 0, +1, or -1). These are specified by the user and are used to create weighted sums or differences of the beta weights, which in turn are evaluated for statistical significance. In the first model for the t-test that we discussed in the previous mail, the hypothesis that B>A would be assessed by a contrast vector like [ 0 +1 ], assuming that the first regressor is the intercept and the second regressor codes 1 for group B and 0 for group A. Keep in mind that in multi-variable regression models, the interpretation of (sums or differences) of parameter estimates is conditional on all other estimates being zero. So in a longitudinal model, for example, it is not the overall mean of e.g. A or B, but the mean at time zero. > 2.Is there any P-value for the lme_fit_FS function to present the > quality of the fitting? No, not really. I also don't think that goodness of fit would be assessed by means of a p-value / hypothesis test, but rather by computing the R^2 statistic. For the LME tools, this needs to be calculated manually, I believe. > 3.As you said before, if I have 3 group A,B,C for this model, and > group A is reference group, the regressor1 is the mean of group A, > and regressor2 and 3 reflect the difference between group A and B,C. > But if I want to know the difference between B and C, what should I > do. From the F-test, there only have a P-value to reflect how > different between group B and C, I wonder can I compute a value the > same as regressor 2 to reflect the difference? To get the difference between two non-reference groups, you would specify a 'difference contrast', which has -1 and +1 at the appropriate columns, and zeros otherwise. Best regards, Kersten > Thanks! > > Best regards, > Guodong > > > > > > > -- > > > > Date: Tue, 5 Nov 2019 09:48:06 + > > From: "Diers, Kersten /DZNE" > > Subject: Re: [Freesurfer] LME model contrast matrix (Diers, Kersten > > /DZNE) > > To: "freesurfer@nmr.mgh.harvard.edu" > u> > > Message-ID: <1572947286.4016.34.ca...@dzne.de> > > Content-Type: text/plain; charset="utf-8" > > > > External Email - Use Caution > > > > Hello Guodong, > > > > consider as an analogy a two-sample t-test, where we simply compare > > two > > groups A and B: > > > > If formulated as a regression problem, a commonly used model matrix > > for > > this test (but others are possible, too) will consist of two > > columns, > > one being all ones (the intercept), the other being zero for group > > A > > and one for group B. > > > > The beta value for the first regressor should reflect the mean for > > group A (which is chosen as the reference group), and the beta > > value > > for the second regressor should reflect the difference between > > group A > > and B, which is the primary interest for this comparison. To get > > the > > mean for group B, one would need to add the beta weights of the two > > regressors. > > > > The LME design matrices follow the same logic. > > > > Alternatively, as said before, other design matrices are possible. > > In > > the above toy example, one could also use a matrix with two > > columns, > > where column 1 is one for group A and zero for group B, and column > > 2 is > > zero for group A and one for group B, thus omitting the overall > > intercept. Then, the beta weights would directly reflect the means > > of A > > and B. To get the difference between groups A and B, one would need > > to > > subtract the beta weights. > > > > Mathematically, the two above models are equivalent. This also > > implies > > that one should not specify a model where there is an intercept, a > > regressor for group A, and a regressor for group B, because in this > > case, the regressors would be linearly dependent. Since having an > > overall intercept is advantageous (especially in more complex > > modelling > > situations than this toy example), the first model is the preferred > > one. > > > > Hope this helps, > > >
